6-160151834-C-A

Variant names:

• chr6-160151834-C-A
• rs622342
• NM_003057.3:c.1386-2964C>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.1386-2964C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,082 control chromosomes in the GnomAD database, including 37,841 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 (37841 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 102 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003057.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A1	NM_003057.3	MANE Select	c.1386-2964C>A		intron	N/A	NP_003048.1
	SLC22A1	NM_153187.2		c.1386-4141C>A		intron	N/A	NP_694857.1
	SLC22A1	NM_001437335.1		c.1386-6682C>A		intron	N/A	NP_001424264.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A1	ENST00000366963.9	TSL:1 MANE Select	c.1386-2964C>A		intron	N/A	ENSP00000355930.4
	SLC22A1	ENST00000324965.8	TSL:5	c.1386-4141C>A		intron	N/A	ENSP00000318103.4
	SLC22A1	ENST00000457470.6	TSL:5	c.1386-6682C>A		intron	N/A	ENSP00000409557.2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106459 AN: 151964 Hom.: 37808 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.673

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: 0.701 AC: 106549 AN: 152082 Hom.: 37841 Cov.: 32 AF XY: 0.703 AC XY: 52262 AN XY: 74346

African (AFR) AF: 0.811 AC: 33662 AN: 41510

American (AMR) AF: 0.647 AC: 9888 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4364 AN: 5186

South Asian (SAS) AF: 0.748 AC: 3609 AN: 4828

European-Finnish (FIN) AF: 0.673 AC: 7092 AN: 10536

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42827 AN: 67952

Other (OTH) AF: 0.718 AC: 1520 AN: 2116

Alfa AF: 0.657 Hom.: 126721

Bravo AF: 0.705

Asia WGS AF: 0.810 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.15
PhyloP100		-0.39
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: rs622342; hg19: chr6-160572866;