Genetic Variant SLC22A11:c.1059-957C>T (chr11-64566642-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018484.4(SLC22A11):c.1059-957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,998 control chromosomes in the GnomAD database, including 12,775 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 12762 hom., cov: 31)

Exomes 𝑓: 0.37 ( 13 hom. )

Consequence

SLC22A11
NM_018484.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.858

Publications

72 publications found

Variant links:

Genes affected

SLC22A11 (HGNC:18120): (solute carrier family 22 member 11) The protein encoded by this gene is involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. The encoded protein is an integral membrane protein and is found mainly in the kidney and in the placenta, where it may act to prevent potentially harmful organic anions from reaching the fetus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

SLC22A11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC22A11	NM_018484.4 link	c.1059-957C>T	intron_variant	Intron 6 of 9	ENST00000301891.9	NP_060954.1	Q9NSA0-1
SLC22A11	NM_001307985.2 link	c.1058+1305C>T	intron_variant	Intron 6 of 7		NP_001294914.1	Q9NSA0-2
SLC22A11	XM_011545167.2 link	c.660-957C>T	intron_variant	Intron 5 of 8		XP_011543469.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC22A11	ENST00000301891.9 link	c.1059-957C>T	intron_variant	Intron 6 of 9	1	NM_018484.4	ENSP00000301891.4	Q9NSA0-1
SLC22A11	ENST00000460745.1 link	n.1788C>T	non_coding_transcript_exon_variant	Exon 4 of 4	2
SLC22A11	ENST00000377581.7 link	c.1059-957C>T	intron_variant	Intron 6 of 8	5		ENSP00000366804.3	A6NCG2
SLC22A11	ENST00000377585.7 link	c.1058+1305C>T	intron_variant	Intron 6 of 7	2		ENSP00000366809.3	Q9NSA0-2

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55653

AN:

151724

Hom.:

12767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.511

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.0199

Gnomad SAS

AF:

0.369

Gnomad FIN

AF:

0.425

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.372

GnomAD4 exome

AF:

0.370

AC:

AN:

154

Hom.:

Cov.:

AF XY:

0.311

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.542

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.463

AC:

AN:

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.366

AC:

55649

AN:

151844

Hom.:

12762

Cov.:

AF XY:

0.361

AC XY:

26762

AN XY:

74182

show subpopulations

African (AFR)

AF:

0.132

AC:

5448

AN:

41404

American (AMR)

AF:

0.315

AC:

4804

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.534

AC:

1852

AN:

3466

East Asian (EAS)

AF:

0.0200

AC:

103

AN:

5156

South Asian (SAS)

AF:

0.370

AC:

1777

AN:

4804

European-Finnish (FIN)

AF:

0.425

AC:

4473

AN:

10536

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.527

AC:

35820

AN:

67912

Other (OTH)

AF:

0.368

AC:

773

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1537

3074

4612

6149

7686

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.467

Hom.:

55727

Bravo

AF:

0.345

Asia WGS

AF:

0.169

AC:

588

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.8

(source)

DANN

Benign

0.86

PhyloP100

-0.86

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over