6-160348247-C-T

Variant names:

• chr6-160348247-C-T
• rs58601841
• NM_021977.4:c.-173C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000275300.3(SLC22A3):​c.-173C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000678 in 590,094 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000068 (0 hom.)
• Consequence: SLC22A3 ENST00000275300.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000275300.3. 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.-173C>T		upstream_gene	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.-173C>T		upstream_gene	N/A	ENSP00000275300.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000678 AC: 4 AN: 590094 Hom.: 0 Cov.: 8 AF XY: 0.00000351 AC XY: 1 AN XY: 284790

African (AFR) AF: 0.00 AC: 0 AN: 12378

American (AMR) AF: 0.00 AC: 0 AN: 5680

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8804

East Asian (EAS) AF: 0.00 AC: 0 AN: 17812

South Asian (SAS) AF: 0.00 AC: 0 AN: 10326

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17798

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1772

European-Non Finnish (NFE) AF: 0.00000815 AC: 4 AN: 490640

Other (OTH) AF: 0.00 AC: 0 AN: 24884

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.4
DANN	Benign	0.97
PhyloP100		-1.9
PromoterAI		-0.040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs58601841; hg19: chr6-160769279;