11-62989641-G-A

Position:

• chr11-62989641-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000539841.1(SLC22A8):​n.7091C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,134 control chromosomes in the GnomAD database, including 4,128 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 0.22 (4126 hom., cov: 32)
  • Exomes 𝑓: 0.25 (2 hom.)
• Consequence: SLC22A8 ENST00000539841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A8	ENST00000539841.1	n.7091C>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33866 AN: 151960 Hom.: 4114 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.250 AC: 14 AN: 56 Hom.: 2 Cov.: 0 AF XY: 0.214 AC XY: 6 AN XY: 28

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.223 AC: 33900 AN: 152078 Hom.: 4126 Cov.: 32 AF XY: 0.223 AC XY: 16593 AN XY: 74356

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.234

Alfa AF: 0.245 Hom.: 6188

Bravo AF: 0.219

Asia WGS AF: 0.290 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955434; hg19: chr11-62757113;