chr6-160153503-C-A

Variant names:

• chr6-160153503-C-A
• rs650284
• NM_003057.3:c.1386-1295C>A

Variant summary

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

The NM_003057.3(SLC22A1):​c.1386-1295C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,064 control chromosomes in the GnomAD database, including 37,759 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 0.70 (37759 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1386-1295C>A		intron_variant	Intron 8 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1386-2472C>A		intron_variant	Intron 8 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.1386-5013C>A		intron_variant	Intron 8 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.1386-1295C>A		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.1386-1295C>A		intron_variant	Intron 8 of 10	1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106338 AN: 151946 Hom.: 37726 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.700 AC: 106427 AN: 152064 Hom.: 37759 Cov.: 32 AF XY: 0.702 AC XY: 52186 AN XY: 74360

African (AFR) AF: 0.810 AC: 33609 AN: 41486

American (AMR) AF: 0.648 AC: 9904 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3468

East Asian (EAS) AF: 0.842 AC: 4361 AN: 5178

South Asian (SAS) AF: 0.743 AC: 3573 AN: 4812

European-Finnish (FIN) AF: 0.666 AC: 7039 AN: 10564

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42836 AN: 67948

Other (OTH) AF: 0.719 AC: 1519 AN: 2114

Alfa AF: 0.657 Hom.: 42360

Bravo AF: 0.705

Asia WGS AF: 0.812 AC: 2818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.27
PhyloP100		-0.72
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: rs650284; hg19: chr6-160574535;