6-160144971-G-T

Variant names:

• chr6-160144971-G-T
• rs644992
• NM_003057.3:c.1385+1322G>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.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
• 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]

ENSG00000301636 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1385+1322G>T		intron_variant	Intron 8 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1385+1322G>T		intron_variant	Intron 8 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.1385+1322G>T		intron_variant	Intron 8 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.1385+1322G>T		intron_variant	Intron 8 of 11		XP_005267160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A1	ENST00000366963.9	c.1385+1322G>T		intron_variant	Intron 8 of 10	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

African (AFR) AF: 0.398 AC: 16493 AN: 41436

American (AMR) AF: 0.478 AC: 7295 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3466

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5160

South Asian (SAS) AF: 0.449 AC: 2160 AN: 4808

European-Finnish (FIN) AF: 0.359 AC: 3774 AN: 10522

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29220 AN: 67936

Other (OTH) AF: 0.455 AC: 961 AN: 2112

Alfa AF: 0.426 Hom.: 3821

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
PhyloP100		-0.73
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: rs644992; hg19: chr6-160566003;