6-35944509-AAATAAT-A

Position:

• chr6-35944509-AAATAAT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_052961.4(SLC26A8):​c.2473-175_2473-170del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.340

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A8	NM_052961.4	c.2473-175_2473-170del		intron_variant		ENST00000490799.6	NP_443193.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A8	ENST00000490799.6	c.2473-175_2473-170del		intron_variant		1	NM_052961.4	ENSP00000417638	P1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 30463 AN: 147800 Hom.: 3447 Cov.: 23

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.: 23 AF XY: 0.205 AC XY: 14761 AN XY: 71946

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.201

Alfa AF: 0.0713 Hom.: 79

Asia WGS AF: 0.209 AC: 720 AN: 3454

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58506796; hg19: chr6-35912286;