11-63016354-T-G

Variant names:

• chr11-63016354-T-G
• rs948979
• ENST00000946794.1:c.-26+296A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000946794.1(SLC22A8):​c.-26+296A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 151,836 control chromosomes in the GnomAD database, including 40,470 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 0.73 (40470 hom., cov: 29)
• Consequence: SLC22A8 ENST00000946794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 7 publications found

Genes affected

SLC22A8 (HGNC:10972): (solute carrier family 22 member 8) This gene encodes a protein 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 appears to be localized to the basolateral membrane of the kidney. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, May 2010]

ENSG00000301851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000946794.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A8	ENST00000946794.1		c.-26+296A>C		intron	N/A	ENSP00000616853.1
	ENSG00000301851	ENST00000782248.1		n.847-9551T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110288 AN: 151718 Hom.: 40444 Cov.: 29

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.727 AC: 110367 AN: 151836 Hom.: 40470 Cov.: 29 AF XY: 0.730 AC XY: 54112 AN XY: 74170

African (AFR) AF: 0.630 AC: 26072 AN: 41376

American (AMR) AF: 0.782 AC: 11959 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2662 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4269 AN: 5122

South Asian (SAS) AF: 0.744 AC: 3563 AN: 4790

European-Finnish (FIN) AF: 0.759 AC: 8013 AN: 10554

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51380 AN: 67922

Other (OTH) AF: 0.731 AC: 1539 AN: 2104

Alfa AF: 0.745 Hom.: 186914

Bravo AF: 0.723

Asia WGS AF: 0.778 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs948979; hg19: chr11-62783826; COSMIC: COSV60327339;