chr6-160429879-C-T

Variant names:

• chr6-160429879-C-T
• rs2661834
• NM_021977.4:c.976-6901C>T

Variant summary

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

The NM_021977.4(SLC22A3):​c.976-6901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,544 control chromosomes in the GnomAD database, including 5,419 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 0.26 (5419 hom., cov: 31)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	NM_021977.4	MANE Select	c.976-6901C>T		intron	N/A	NP_068812.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	ENST00000275300.3	TSL:1 MANE Select	c.976-6901C>T		intron	N/A	ENSP00000275300.2
	SLC22A3	ENST00000855214.1		c.1066-6901C>T		intron	N/A	ENSP00000525273.1
	SLC22A3	ENST00000855213.1		c.430-6901C>T		intron	N/A	ENSP00000525272.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39569 AN: 151440 Hom.: 5419 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.261 AC: 39585 AN: 151544 Hom.: 5419 Cov.: 31 AF XY: 0.265 AC XY: 19589 AN XY: 74028

African (AFR) AF: 0.194 AC: 8018 AN: 41314

American (AMR) AF: 0.208 AC: 3168 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.360 AC: 1861 AN: 5166

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4812

European-Finnish (FIN) AF: 0.298 AC: 3083 AN: 10358

Middle Eastern (MID) AF: 0.392 AC: 112 AN: 286

European-Non Finnish (NFE) AF: 0.286 AC: 19446 AN: 67884

Other (OTH) AF: 0.292 AC: 618 AN: 2114

Alfa AF: 0.272 Hom.: 9777

Bravo AF: 0.253

Asia WGS AF: 0.366 AC: 1270 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		0.46
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: rs2661834; hg19: chr6-160850911;