6-160157882-C-T

Variant names:

• chr6-160157882-C-T
• rs609468
• NM_003057.3:c.1599-634C>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.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
• Publications: 10 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=-0.91).
• 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 rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1599-634C>T		intron_variant	Intron 10 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1486-634C>T		intron_variant	Intron 9 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.1386-634C>T		intron_variant	Intron 8 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.1687-634C>T		intron_variant	Intron 11 of 11		XP_005267160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1599-634C>T		intron_variant	Intron 10 of 10	1	NM_003057.3	ENSP00000355930.4

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

African (AFR) AF: 0.344 AC: 14253 AN: 41444

American (AMR) AF: 0.340 AC: 5185 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3460

East Asian (EAS) AF: 0.520 AC: 2684 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1764 AN: 4810

European-Finnish (FIN) AF: 0.271 AC: 2866 AN: 10558

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15094 AN: 67956

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.257 Hom.: 8049

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
PhyloP100		-1.5
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: rs609468; hg19: chr6-160578914;