rs1867350

Variant names:

• chr6-160142173-C-T
• rs1867350
• NM_003057.3:c.1277-1368C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003057.3(SLC22A1):​c.1277-1368C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,218 control chromosomes in the GnomAD database, including 711 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 0.056 (711 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 7 publications found

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]

ENSG00000301636 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1277-1368C>T		intron_variant	Intron 7 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1277-1368C>T		intron_variant	Intron 7 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.1277-1368C>T		intron_variant	Intron 7 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.1277-1368C>T		intron_variant	Intron 7 of 11		XP_005267160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1277-1368C>T		intron_variant	Intron 7 of 10	1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8458 AN: 152100 Hom.: 711 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0556 AC: 8465 AN: 152218 Hom.: 711 Cov.: 32 AF XY: 0.0591 AC XY: 4401 AN XY: 74424

African (AFR) AF: 0.0107 AC: 444 AN: 41532

American (AMR) AF: 0.145 AC: 2211 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1934 AN: 5164

South Asian (SAS) AF: 0.0980 AC: 473 AN: 4826

European-Finnish (FIN) AF: 0.0555 AC: 588 AN: 10598

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2652 AN: 68014

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0466 Hom.: 479

Bravo AF: 0.0644

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.53
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1867350; hg19: chr6-160563205;