6-160144971-G-T

Position:

• chr6-160144971-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003057.3(SLC22A1):​c.1385+1322G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,910 control chromosomes in the GnomAD database, including 13,697 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 0.42 (13697 hom., cov: 33)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1385+1322G>T		intron_variant		ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1385+1322G>T		intron_variant			NP_694857.1
SLC22A1	XM_005267103.3	c.1385+1322G>T		intron_variant			XP_005267160.1
SLC22A1	XM_006715552.3	c.1385+1322G>T		intron_variant			XP_006715615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1385+1322G>T		intron_variant		1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64206 AN: 151790 Hom.: 13679 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.423 AC: 64266 AN: 151910 Hom.: 13697 Cov.: 33 AF XY: 0.423 AC XY: 31411 AN XY: 74248

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.455

Alfa AF: 0.427 Hom.: 1735

Bravo AF: 0.430

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs644992; hg19: chr6-160566003;