rs7750592

Variant names:

• chr6-160148750-T-C
• rs7750592
• NM_003057.3:c.1385+5101T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-160148750-T-C
• chr6-160148750-T-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.1385+5101T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,668 control chromosomes in the GnomAD database, including 14,597 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 0.43 (14597 hom., cov: 30)
• Consequence: SLC22A1 NM_003057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.69
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A1	NM_003057.3	c.1385+5101T>C		intron_variant	Intron 8 of 10	ENST00000366963.9	NP_003048.1
SLC22A1	NM_153187.2	c.1385+5101T>C		intron_variant	Intron 8 of 9		NP_694857.1
SLC22A1	NM_001437335.1	c.1385+5101T>C		intron_variant	Intron 8 of 8		NP_001424264.1
SLC22A1	XM_005267103.3	c.1385+5101T>C		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+5101T>C		intron_variant	Intron 8 of 10	1	NM_003057.3	ENSP00000355930.4

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65638 AN: 151552 Hom.: 14577 Cov.: 30

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.433 AC: 65706 AN: 151668 Hom.: 14597 Cov.: 30 AF XY: 0.429 AC XY: 31766 AN XY: 74114

African (AFR) AF: 0.527 AC: 21781 AN: 41326

American (AMR) AF: 0.322 AC: 4901 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1729 AN: 5120

South Asian (SAS) AF: 0.386 AC: 1851 AN: 4800

European-Finnish (FIN) AF: 0.392 AC: 4119 AN: 10508

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27788 AN: 67884

Other (OTH) AF: 0.441 AC: 931 AN: 2112

Alfa AF: 0.271 Hom.: 605

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.57
PhyloP100		-4.7
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: rs7750592; hg19: chr6-160569782;