rs10792367

Variant names:

• chr11-62991327-C-G
• rs10792367
• ENST00000539841.1:n.5405G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539841.1. 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	ENST00000539841.1	TSL:1	n.5405G>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301851	ENST00000782248.1		n.846+25782C>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.486 AC: 20085 AN: 41302

American (AMR) AF: 0.318 AC: 4842 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1484 AN: 3462

East Asian (EAS) AF: 0.505 AC: 2602 AN: 5150

South Asian (SAS) AF: 0.542 AC: 2601 AN: 4800

European-Finnish (FIN) AF: 0.503 AC: 5290 AN: 10514

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28845 AN: 67900

Other (OTH) AF: 0.437 AC: 921 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.4
DANN	Benign	0.51
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10792367; hg19: chr11-62758799;