rs3798170

Variant names:

• chr6-160135153-A-G
• rs3798170
• NM_003057.3:c.839+1028A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-160135153-A-G
• chr6-160135153-A-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.839+1028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 151,720 control chromosomes in the GnomAD database, including 116 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 0.028 (116 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.839+1028A>G		intron_variant	Intron 4 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.839+1028A>G		intron_variant	Intron 4 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.839+1028A>G		intron_variant	Intron 4 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.839+1028A>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+1028A>G		intron_variant	Intron 4 of 10	1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4243 AN: 151602 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.00808

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0207

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

GnomAD4 genome AF: 0.0280 AC: 4251 AN: 151720 Hom.: 116 Cov.: 32 AF XY: 0.0306 AC XY: 2267 AN XY: 74132

African (AFR) AF: 0.0365 AC: 1511 AN: 41346

American (AMR) AF: 0.0341 AC: 520 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.129 AC: 664 AN: 5156

South Asian (SAS) AF: 0.0842 AC: 403 AN: 4786

European-Finnish (FIN) AF: 0.00808 AC: 85 AN: 10520

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1005 AN: 67900

Other (OTH) AF: 0.0204 AC: 43 AN: 2104

Alfa AF: 0.0271 Hom.: 12

Bravo AF: 0.0288

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.081
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: rs3798170; hg19: chr6-160556185;