chr6-160377016-A-G

Variant names:

• chr6-160377016-A-G
• rs61131294
• NM_021977.4:c.430-20963A>G

Variant summary

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

The NM_021977.4(SLC22A3):​c.430-20963A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,070 control chromosomes in the GnomAD database, including 3,570 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 0.21 (3570 hom., cov: 32)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 4 publications found

Genes affected

SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) 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. [provided by RefSeq, Jul 2008]

ENSG00000287656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A3	NM_021977.4	c.430-20963A>G		intron_variant	Intron 1 of 10	ENST00000275300.3	NP_068812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300.3	c.430-20963A>G		intron_variant	Intron 1 of 10	1	NM_021977.4	ENSP00000275300.2
ENSG00000287656	ENST00000663900.1	n.1100-6570T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32125 AN: 151952 Hom.: 3563 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.211 AC: 32147 AN: 152070 Hom.: 3570 Cov.: 32 AF XY: 0.216 AC XY: 16043 AN XY: 74314

African (AFR) AF: 0.159 AC: 6584 AN: 41504

American (AMR) AF: 0.313 AC: 4783 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5166

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4814

European-Finnish (FIN) AF: 0.268 AC: 2826 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13885 AN: 67968

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.213 Hom.: 451

Bravo AF: 0.212

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-1.7
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: rs61131294; hg19: chr6-160798048;