rs609468

Positions:

• chr6-160157882-C-T

Variant summary

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

The NM_003057.3(SLC22A1):​c.1599-634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,972 control chromosomes in the GnomAD database, including 6,788 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 0.29 (6788 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

SLC22A1 (HGNC:10963): (solute carrier family 22 member 1) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A1	NM_003057.3	c.1599-634C>T		intron_variant		ENST00000366963.9
SLC22A1	NM_153187.2	c.1486-634C>T		intron_variant
SLC22A1	XM_005267103.3	c.1687-634C>T		intron_variant
SLC22A1	XM_006715552.3	c.1386-634C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1599-634C>T		intron_variant		1	NM_003057.3	P1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43476 AN: 151854 Hom.: 6780 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.286 AC: 43519 AN: 151972 Hom.: 6788 Cov.: 32 AF XY: 0.293 AC XY: 21725 AN XY: 74270

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.294

Alfa AF: 0.241 Hom.: 4502

Bravo AF: 0.295

Asia WGS AF: 0.466 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs609468; hg19: chr6-160578914;