rs10792367

Positions:

• chr11-62991327-C-G

Variant summary

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

The ENST00000539841.1(SLC22A8):​n.5405G>C 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 0.444 in 151,660 control chromosomes in the GnomAD database, including 15,325 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 0.44 (15323 hom., cov: 30)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: SLC22A8 ENST00000539841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

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=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A8	ENST00000539841.1	n.5405G>C		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67286 AN: 151536 Hom.: 15285 Cov.: 30

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.433

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.444 AC: 67370 AN: 151654 Hom.: 15323 Cov.: 30 AF XY: 0.447 AC XY: 33133 AN XY: 74070

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.437

Alfa AF: 0.426 Hom.: 1769

Bravo AF: 0.430

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792367; hg19: chr11-62758799;