dbSNP rs9457880: LOC105378088:n.2082C>A (chr6-160277707-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001744437.2(LOC105378088):n.2082C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0432 in 152,192 control chromosomes in the GnomAD database, including 265 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 0.043 ( 265 hom., cov: 32)

Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

LOC105378088
XR_001744437.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.961

Variant links:

Genes affected

LOC105378088 (HGNC:):

LOC105378088 links:

SLC22A2 (HGNC:10966): (solute carrier family 22 member 2) 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. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

SLC22A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378088	XR_001744437.2 link	n.2082C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366952.1 link	c.-1551G>T		upstream_gene_variant		5		ENSP00000355919.1		Q5T7Q5

Frequencies

GnomAD3 genomes

AF:

0.0433

AC:

6576

AN:

152042

Hom.:

265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0123

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0204

Gnomad ASJ

AF:

0.0352

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.0772

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0441

Gnomad OTH

AF:

0.0445

GnomAD4 exome

AF:

0.0625

AC:

AN:

Hom.:

AF XY:

0.0769

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0769

GnomAD4 genome

AF:

0.0432

AC:

6574

AN:

152160

Hom.:

265

Cov.:

AF XY:

0.0477

AC XY:

3547

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0123

Gnomad4 AMR

AF:

0.0204

Gnomad4 ASJ

AF:

0.0352

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.0772

Gnomad4 NFE

AF:

0.0441

Gnomad4 OTH

AF:

0.0440

Alfa

AF:

0.0429

Hom.:

Bravo

AF:

0.0355

Asia WGS

AF:

0.188

AC:

652

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.094

DANN

Benign

0.79

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over