Genetic Variant SLC26A8:c.2473-175_2473-170delATTATT (chr6-35944509-AAATAAT-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_052961.4(SLC26A8):c.2473-175_2473-170delATTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 147,804 control chromosomes in the GnomAD database, including 3,441 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.21 ( 3441 hom., cov: 23)

Consequence

SLC26A8
NM_052961.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.340

Publications

0 publications found

Variant links:

Genes affected

SLC26A8 (HGNC:14468): (solute carrier family 26 member 8) This gene encodes a member of the SLC26 gene family of anion transporters. Family members are well conserved in gene structure and protein length yet have markedly different tissue expression patterns. The expression of this gene appears to be restricted to spermatocytes. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jul 2010]

SLC26A8 Gene-Disease associations (from GenCC):

non-syndromic male infertility due to sperm motility disorder
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia
spermatogenic failure 3
Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

SLC26A8 links:

ENSG00000304790 (HGNC:):

ENSG00000304790 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 6-35944509-AAATAAT-A is Benign according to our data. Variant chr6-35944509-AAATAAT-A is described in ClinVar as Benign. ClinVar VariationId is 1277385.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052961.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC26A8	NM_052961.4	MANE Select	c.2473-175_2473-170delATTATT	intron	N/A	NP_443193.1	Q96RN1-1
SLC26A8	NM_001193476.2		c.2473-175_2473-170delATTATT	intron	N/A	NP_001180405.1	Q96RN1-1
SLC26A8	NM_138718.3		c.2158-175_2158-170delATTATT	intron	N/A	NP_619732.2	Q96RN1-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC26A8	ENST00000490799.6	TSL:1 MANE Select	c.2473-175_2473-170delATTATT	intron	N/A	ENSP00000417638.1	Q96RN1-1
SLC26A8	ENST00000394602.6	TSL:1	c.2158-175_2158-170delATTATT	intron	N/A	ENSP00000378100.2	Q96RN1-2
SLC26A8	ENST00000355574.6	TSL:2	c.2473-175_2473-170delATTATT	intron	N/A	ENSP00000347778.2	Q96RN1-1

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

30463

AN:

147800

Hom.:

3447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.315

Gnomad NFE

AF:

0.256

Gnomad OTH

AF:

0.201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.206

AC:

30442

AN:

147804

Hom.:

3441

Cov.:

AF XY:

0.205

AC XY:

14761

AN XY:

71946

show subpopulations

African (AFR)

AF:

0.118

AC:

4803

AN:

40698

American (AMR)

AF:

0.186

AC:

2749

AN:

14780

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

709

AN:

3444

East Asian (EAS)

AF:

0.220

AC:

1123

AN:

5094

South Asian (SAS)

AF:

0.217

AC:

1030

AN:

4736

European-Finnish (FIN)

AF:

0.247

AC:

2167

AN:

8768

Middle Eastern (MID)

AF:

0.302

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.256

AC:

17157

AN:

67086

Other (OTH)

AF:

0.201

AC:

406

AN:

2022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1138

2277

3415

4554

5692

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<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:

0.0713

Hom.:

Asia WGS

AF:

0.209

AC:

720

AN:

3454

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over