rs3120137

Variant names:

• chr6-160350160-G-A
• rs3120137
• NM_021977.4:c.429+1312G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-160350160-G-A
• chr6-160350160-G-C
• chr6-160350160-G-T

Variant summary

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

The NM_021977.4(SLC22A3):​c.429+1312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 149,914 control chromosomes in the GnomAD database, including 947 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 0.092 (947 hom., cov: 32)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 14 publications found

Genes affected

SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) 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. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A3	NM_021977.4	c.429+1312G>A		intron_variant	Intron 1 of 10	ENST00000275300.3	NP_068812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300.3	c.429+1312G>A		intron_variant	Intron 1 of 10	1	NM_021977.4	ENSP00000275300.2

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13758 AN: 149792 Hom.: 947 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.000786

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.00987

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0917 AC: 13750 AN: 149914 Hom.: 947 Cov.: 32 AF XY: 0.0864 AC XY: 6325 AN XY: 73182

African (AFR) AF: 0.0267 AC: 1082 AN: 40600

American (AMR) AF: 0.0692 AC: 1043 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.0358 AC: 123 AN: 3438

East Asian (EAS) AF: 0.000788 AC: 4 AN: 5074

South Asian (SAS) AF: 0.0111 AC: 52 AN: 4666

European-Finnish (FIN) AF: 0.113 AC: 1164 AN: 10286

Middle Eastern (MID) AF: 0.0106 AC: 3 AN: 284

European-Non Finnish (NFE) AF: 0.148 AC: 10012 AN: 67504

Other (OTH) AF: 0.0757 AC: 158 AN: 2088

Alfa AF: 0.111 Hom.: 1961

Bravo AF: 0.0840

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.42
PhyloP100		-1.7
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: rs3120137; hg19: chr6-160771192;