6-160260361-A-G

Variant names:

• chr6-160260361-A-G
• rs3127573
• ENST00000366952.1:c.-970T>C

Variant summary

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

The ENST00000366952.1(SLC22A2):​c.-970T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,200 control chromosomes in the GnomAD database, including 1,205 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 0.12 (1205 hom., cov: 33)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: SLC22A2 ENST00000366952.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 45 publications found

Genes affected

SLC22A2 (HGNC:10966): (solute carrier family 22 member 2) 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. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366952.1	c.-970T>C		5_prime_UTR_variant	Exon 2 of 8	5		ENSP00000355919.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18234 AN: 152076 Hom.: 1202 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0990

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.120 AC: 18253 AN: 152194 Hom.: 1205 Cov.: 33 AF XY: 0.115 AC XY: 8561 AN XY: 74392

African (AFR) AF: 0.155 AC: 6447 AN: 41516

American (AMR) AF: 0.0765 AC: 1170 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.101 AC: 524 AN: 5182

South Asian (SAS) AF: 0.0634 AC: 306 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1098 AN: 10576

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8257 AN: 68004

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.116 Hom.: 4688

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-0.89
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3127573; hg19: chr6-160681393; COSMIC: COSV65267713; COSMIC: COSV65267713;