rs3798168

Variant names:

• chr6-160138775-C-A
• rs3798168
• NM_003057.3:c.1062-878C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-160138775-C-A
• chr6-160138775-C-G

Variant summary

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

The NM_003057.3(SLC22A1):​c.1062-878C>A 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 152,292 control chromosomes in the GnomAD database, including 720 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 (720 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 12 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1062-878C>A		intron_variant	Intron 6 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1062-878C>A		intron_variant	Intron 6 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.1062-878C>A		intron_variant	Intron 6 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.1062-878C>A		intron_variant	Intron 6 of 11		XP_005267160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1062-878C>A		intron_variant	Intron 6 of 10	1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8458 AN: 152174 Hom.: 719 Cov.: 32

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0556 AC: 8466 AN: 152292 Hom.: 720 Cov.: 32 AF XY: 0.0592 AC XY: 4406 AN XY: 74462

African (AFR) AF: 0.0103 AC: 430 AN: 41580

American (AMR) AF: 0.144 AC: 2207 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3466

East Asian (EAS) AF: 0.377 AC: 1953 AN: 5176

South Asian (SAS) AF: 0.0983 AC: 475 AN: 4830

European-Finnish (FIN) AF: 0.0557 AC: 591 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0389 AC: 2647 AN: 68030

Other (OTH) AF: 0.0621 AC: 131 AN: 2108

Alfa AF: 0.0458 Hom.: 562

Bravo AF: 0.0643

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.99
DANN	Benign	0.78
PhyloP100		-1.0
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: rs3798168; hg19: chr6-160559807;