chr6-160157828-T-C

Variant names:

• chr6-160157828-T-C
• rs1564348
• NM_003057.3:c.1599-688T>C

Variant summary

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

The NM_003057.3(SLC22A1):​c.1599-688T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,208 control chromosomes in the GnomAD database, including 1,738 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 0.14 (1738 hom., cov: 32)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 113 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 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.1599-688T>C		intron	N/A	NP_003048.1
	SLC22A1	NM_153187.2		c.1486-688T>C		intron	N/A	NP_694857.1
	SLC22A1	NM_001437335.1		c.1386-688T>C		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.1599-688T>C		intron	N/A	ENSP00000355930.4
	SLC22A1	ENST00000324965.8	TSL:5	c.1486-688T>C		intron	N/A	ENSP00000318103.4
	SLC22A1	ENST00000457470.6	TSL:5	c.1386-688T>C		intron	N/A	ENSP00000409557.2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21746 AN: 152090 Hom.: 1733 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.143 AC: 21768 AN: 152208 Hom.: 1738 Cov.: 32 AF XY: 0.144 AC XY: 10703 AN XY: 74416

African (AFR) AF: 0.109 AC: 4522 AN: 41538

American (AMR) AF: 0.208 AC: 3181 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5184

South Asian (SAS) AF: 0.132 AC: 637 AN: 4814

European-Finnish (FIN) AF: 0.152 AC: 1614 AN: 10598

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11047 AN: 67994

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.154 Hom.: 8807

Bravo AF: 0.146

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.58
PhyloP100		-1.3
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: rs1564348; hg19: chr6-160578860;