chr6-160153770-A-G

Variant names:

• chr6-160153770-A-G
• rs1443844
• NM_003057.3:c.1386-1028A>G

Variant summary

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

The NM_003057.3(SLC22A1):​c.1386-1028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,846 control chromosomes in the GnomAD database, including 14,885 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 0.44 (14885 hom., cov: 31)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 12 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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.1386-1028A>G		intron	N/A	NP_003048.1
	SLC22A1	NM_153187.2		c.1386-2205A>G		intron	N/A	NP_694857.1
	SLC22A1	NM_001437335.1		c.1386-4746A>G		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.1386-1028A>G		intron	N/A	ENSP00000355930.4
	SLC22A1	ENST00000324965.8	TSL:5	c.1386-2205A>G		intron	N/A	ENSP00000318103.4
	SLC22A1	ENST00000457470.6	TSL:5	c.1386-4746A>G		intron	N/A	ENSP00000409557.2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66060 AN: 151726 Hom.: 14876 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.435 AC: 66109 AN: 151846 Hom.: 14885 Cov.: 31 AF XY: 0.431 AC XY: 31998 AN XY: 74228

African (AFR) AF: 0.541 AC: 22388 AN: 41366

American (AMR) AF: 0.312 AC: 4763 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1840 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5160

South Asian (SAS) AF: 0.381 AC: 1827 AN: 4798

European-Finnish (FIN) AF: 0.394 AC: 4152 AN: 10532

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27740 AN: 67944

Other (OTH) AF: 0.441 AC: 929 AN: 2108

Alfa AF: 0.415 Hom.: 22498

Bravo AF: 0.435

Asia WGS AF: 0.369 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.76
PhyloP100		0.13
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: rs1443844; hg19: chr6-160574802;