rs3798172

Variant names:

• chr6-160135011-C-G
• rs3798172
• NM_003057.3:c.839+886C>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.839+886C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,164 control chromosomes in the GnomAD database, including 481 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 0.068 (481 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.839+886C>G		intron_variant	Intron 4 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.839+886C>G		intron_variant	Intron 4 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.839+886C>G		intron_variant	Intron 4 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.839+886C>G		intron_variant	Intron 4 of 11		XP_005267160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9	c.839+886C>G		intron_variant	Intron 4 of 10	1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10339 AN: 152046 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0681 AC: 10356 AN: 152164 Hom.: 481 Cov.: 32 AF XY: 0.0666 AC XY: 4955 AN XY: 74400

African (AFR) AF: 0.123 AC: 5100 AN: 41476

American (AMR) AF: 0.0691 AC: 1058 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.0338 AC: 175 AN: 5178

South Asian (SAS) AF: 0.0693 AC: 334 AN: 4818

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2959 AN: 67998

Other (OTH) AF: 0.0763 AC: 161 AN: 2110

Alfa AF: 0.0599 Hom.: 49

Bravo AF: 0.0739

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.46
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: rs3798172; hg19: chr6-160556043;