rs884742

Positions:

• chr6-160386400-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000275300.3(SLC22A3):​c.430-11579C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,160 control chromosomes in the GnomAD database, including 16,735 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 0.46 (16735 hom., cov: 34)
• Consequence: SLC22A3 ENST00000275300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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]

LOC124901453 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A3	NM_021977.4	c.430-11579C>A		intron_variant		ENST00000275300.3	NP_068812.1
LOC124901453	XR_007059843.1	n.5754G>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300.3	c.430-11579C>A		intron_variant		1	NM_021977.4	ENSP00000275300	P1
	ENST00000663900.1	n.165+370G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70672 AN: 152042 Hom.: 16721 Cov.: 34

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.465 AC: 70709 AN: 152160 Hom.: 16735 Cov.: 34 AF XY: 0.467 AC XY: 34697 AN XY: 74366

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.469

Alfa AF: 0.481 Hom.: 24094

Bravo AF: 0.462

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs884742; hg19: chr6-160807432; COSMIC: COSV51716470;