dbSNP rs6084312: SLC4A11:p.Thr447Thr (chr20-3230589-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001174089.2(SLC4A11):c.1341G>A(p.Thr447Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,613,710 control chromosomes in the GnomAD database, including 9,686 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 718 hom., cov: 34)

Exomes 𝑓: 0.11 ( 8968 hom. )

Consequence

SLC4A11
NM_001174089.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.197

Publications

19 publications found

Variant links:

Genes affected

SLC4A11 (HGNC:16438): (solute carrier family 4 member 11) This gene encodes a voltage-regulated, electrogenic sodium-coupled borate cotransporter that is essential for borate homeostasis, cell growth and cell proliferation. Mutations in this gene have been associated with a number of endothelial corneal dystrophies including recessive corneal endothelial dystrophy 2, corneal dystrophy and perceptive deafness, and Fuchs endothelial corneal dystrophy. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2010]

SLC4A11 Gene-Disease associations (from GenCC):

corneal dystrophy, Fuchs endothelial, 4
Inheritance: AD Classification: STRONG, LIMITED Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae)
congenital hereditary endothelial dystrophy of cornea
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia, Orphanet
corneal dystrophy-perceptive deafness syndrome
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
Fuchs' endothelial dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SLC4A11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 20-3230589-C-T is Benign according to our data. Variant chr20-3230589-C-T is described in ClinVar as Benign. ClinVar VariationId is 261996.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.197 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001174089.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC4A11	NM_001174089.2	MANE Select	c.1341G>A	p.Thr447Thr	synonymous	Exon 12 of 20	NP_001167560.1	Q8NBS3-3
SLC4A11	NM_001174090.2		c.1470G>A	p.Thr490Thr	synonymous	Exon 12 of 20	NP_001167561.1	Q8NBS3-4
SLC4A11	NM_032034.4		c.1389G>A	p.Thr463Thr	synonymous	Exon 11 of 19	NP_114423.1	Q8NBS3-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC4A11	ENST00000642402.1	MANE Select	c.1341G>A	p.Thr447Thr	synonymous	Exon 12 of 20	ENSP00000493503.1	Q8NBS3-3
SLC4A11	ENST00000380056.7	TSL:1	c.1389G>A	p.Thr463Thr	synonymous	Exon 11 of 19	ENSP00000369396.3	Q8NBS3-1
SLC4A11	ENST00000380059.7	TSL:2	c.1470G>A	p.Thr490Thr	synonymous	Exon 12 of 20	ENSP00000369399.3	Q8NBS3-4

Frequencies

GnomAD3 genomes

AF:

0.0848

AC:

12890

AN:

152062

Hom.:

719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0347

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0863

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.0219

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.0947

GnomAD2 exomes

AF:

0.0864

AC:

21720

AN:

251334

AF XY:

0.0859

show subpopulations

Gnomad AFR exome

AF:

0.0326

Gnomad AMR exome

AF:

0.0651

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.00223

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.105

AC:

153790

AN:

1461528

Hom.:

8968

Cov.:

AF XY:

0.103

AC XY:

74916

AN XY:

727056

show subpopulations

African (AFR)

AF:

0.0316

AC:

1057

AN:

33480

American (AMR)

AF:

0.0693

AC:

3100

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

3334

AN:

26136

East Asian (EAS)

AF:

0.00199

AC:

AN:

39700

South Asian (SAS)

AF:

0.0228

AC:

1964

AN:

86258

European-Finnish (FIN)

AF:

0.111

AC:

5923

AN:

53122

Middle Eastern (MID)

AF:

0.0700

AC:

404

AN:

5768

European-Non Finnish (NFE)

AF:

0.119

AC:

132131

AN:

1111950

Other (OTH)

AF:

0.0960

AC:

5798

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

8748

17496

26245

34993

43741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4528

9056

13584

18112

22640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0847

AC:

12886

AN:

152182

Hom.:

718

Cov.:

AF XY:

0.0833

AC XY:

6200

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0347

AC:

1439

AN:

41522

American (AMR)

AF:

0.0862

AC:

1319

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

408

AN:

3472

East Asian (EAS)

AF:

0.00174

AC:

AN:

5158

South Asian (SAS)

AF:

0.0222

AC:

107

AN:

4830

European-Finnish (FIN)

AF:

0.118

AC:

1248

AN:

10608

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.119

AC:

8065

AN:

67976

Other (OTH)

AF:

0.0938

AC:

198

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

617

1233

1850

2466

3083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.107

Hom.:

2187

Bravo

AF:

0.0799

Asia WGS

AF:

0.0190

AC:

AN:

3478

EpiCase

AF:

0.122

EpiControl

AF:

0.121

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Corneal dystrophy-perceptive deafness syndrome (2)

not provided (2)

not specified (2)

Congenital hereditary endothelial dystrophy of cornea (1)

Corneal dystrophy (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.3

(source)

DANN

Benign

0.47

PhyloP100

-0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over