6-160368264-A-G

Variant names:

• chr6-160368264-A-G
• rs402219
• NM_021977.4:c.429+19416A>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.429+19416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,914 control chromosomes in the GnomAD database, including 6,394 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 0.28 (6394 hom., cov: 31)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 18 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021977.4. 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
	SLC22A3	NM_021977.4	MANE Select	c.429+19416A>G		intron	N/A	NP_068812.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	ENST00000275300.3	TSL:1 MANE Select	c.429+19416A>G		intron	N/A	ENSP00000275300.2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42469 AN: 151796 Hom.: 6381 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.280 AC: 42519 AN: 151914 Hom.: 6394 Cov.: 31 AF XY: 0.284 AC XY: 21063 AN XY: 74228

African (AFR) AF: 0.175 AC: 7253 AN: 41410

American (AMR) AF: 0.365 AC: 5576 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3462

East Asian (EAS) AF: 0.396 AC: 2038 AN: 5144

South Asian (SAS) AF: 0.380 AC: 1827 AN: 4804

European-Finnish (FIN) AF: 0.304 AC: 3209 AN: 10562

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20471 AN: 67952

Other (OTH) AF: 0.309 AC: 651 AN: 2108

Alfa AF: 0.298 Hom.: 29797

Bravo AF: 0.283

Asia WGS AF: 0.381 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.48
PhyloP100		-2.2
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: rs402219; hg19: chr6-160789296;