chr11-63016300-A-G

Variant names:

• chr11-63016300-A-G
• rs3809069
• ENST00000946794.1:c.-26+350T>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+350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,166 control chromosomes in the GnomAD database, including 1,846 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 0.14 (1846 hom., cov: 32)
• Consequence: SLC22A8 ENST00000946794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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+350T>C		intron	N/A	ENSP00000616853.1
	ENSG00000301851	ENST00000782248.1		n.847-9605A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20712 AN: 152048 Hom.: 1841 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.136 AC: 20710 AN: 152166 Hom.: 1846 Cov.: 32 AF XY: 0.139 AC XY: 10327 AN XY: 74384

African (AFR) AF: 0.0362 AC: 1504 AN: 41560

American (AMR) AF: 0.123 AC: 1877 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1522 AN: 5158

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1814 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11209 AN: 67952

Other (OTH) AF: 0.148 AC: 311 AN: 2106

Alfa AF: 0.150 Hom.: 3682

Bravo AF: 0.127

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-1.3
PromoterAI		0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3809069; hg19: chr11-62783772;