Genetic Variant NM_052832.4:c.1141-3642T>C (chr8-91348168-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_052832.4(SLC26A7):c.1141-3642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 215,092 control chromosomes in the GnomAD database, including 4,769 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 0.20 ( 4099 hom., cov: 33)

Exomes 𝑓: 0.14 ( 670 hom. )

Consequence

SLC26A7
NM_052832.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

Publications

10 publications found

Variant links:

Genes affected

SLC26A7 (HGNC:14467): (solute carrier family 26 member 7) This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in gene structure and protein length yet have markedly different tissue expression patterns. This gene has abundant and specific expression in the kidney. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Aug 2013]

SLC26A7 Gene-Disease associations (from GenCC):

congenital hypothyroidism
Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics

SLC26A7 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC26A7	NM_052832.4 link	c.1141-3642T>C	intron_variant	Intron 9 of 18	ENST00000276609.8	NP_439897.1	Q8TE54-1
SLC26A7	NM_134266.2 link	c.1141-3642T>C	intron_variant	Intron 9 of 18		NP_599028.1	Q8TE54-2
SLC26A7	NM_001282356.2 link	c.1141-3642T>C	intron_variant	Intron 10 of 19		NP_001269285.1	Q8TE54-1
SLC26A7	NM_001282357.2 link	c.238-3642T>C	intron_variant	Intron 9 of 18		NP_001269286.1	Q8TE54A0A087WZI7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A7	ENST00000276609.8 link	c.1141-3642T>C		intron_variant	Intron 9 of 18	1	NM_052832.4	ENSP00000276609.3		Q8TE54-1

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30593

AN:

152146

Hom.:

4074

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0845

Gnomad EAS

AF:

0.0211

Gnomad SAS

AF:

0.0964

Gnomad FIN

AF:

0.0998

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.141

AC:

8837

AN:

62826

Hom.:

670

AF XY:

0.141

AC XY:

4316

AN XY:

30714

show subpopulations

African (AFR)

AF:

0.374

AC:

397

AN:

1062

American (AMR)

AF:

0.0610

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.0692

AC:

AN:

448

East Asian (EAS)

AF:

0.0205

AC:

AN:

292

South Asian (SAS)

AF:

0.0932

AC:

121

AN:

1298

European-Finnish (FIN)

AF:

0.0556

AC:

AN:

Middle Eastern (MID)

AF:

0.0776

AC:

AN:

116

European-Non Finnish (NFE)

AF:

0.140

AC:

8025

AN:

57502

Other (OTH)

AF:

0.121

AC:

242

AN:

2008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

393

787

1180

1574

1967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

384

768

1152

1536

1920

<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:

0.201

AC:

30666

AN:

152266

Hom.:

4099

Cov.:

AF XY:

0.195

AC XY:

14492

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.380

AC:

15791

AN:

41534

American (AMR)

AF:

0.144

AC:

2197

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0845

AC:

293

AN:

3468

East Asian (EAS)

AF:

0.0214

AC:

111

AN:

5194

South Asian (SAS)

AF:

0.0969

AC:

468

AN:

4830

European-Finnish (FIN)

AF:

0.0998

AC:

1059

AN:

10616

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10183

AN:

68018

Other (OTH)

AF:

0.184

AC:

388

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1181

2361

3542

4722

5903

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.166

Hom.:

7430

Bravo

AF:

0.214

Asia WGS

AF:

0.0820

AC:

286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.9

(source)

DANN

Benign

0.77

PhyloP100

-0.011

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

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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