Genetic Variant NM_015482.2:c.655-3060A>G (chr6-3418915-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015482.2(SLC22A23):c.655-3060A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,034 control chromosomes in the GnomAD database, including 11,081 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 0.38 ( 11081 hom., cov: 32)

Consequence

SLC22A23
NM_015482.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82

Variant links:

Genes affected

SLC22A23 (HGNC:21106): (solute carrier family 22 member 23) SLC22A23 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 2008]

SLC22A23 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A23	NM_015482.2 link	c.655-3060A>G		intron_variant	Intron 1 of 9	ENST00000406686.8	NP_056297.1	A1A5C7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686.8 link	c.655-3060A>G		intron_variant	Intron 1 of 9	5	NM_015482.2	ENSP00000385028.3		A1A5C7-1

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57464

AN:

151916

Hom.:

11069

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.386

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

GnomAD4 genome

AF:

0.378

AC:

57503

AN:

152034

Hom.:

11081

Cov.:

AF XY:

0.379

AC XY:

28159

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.320

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.423

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.213

Gnomad4 FIN

AF:

0.462

Gnomad4 NFE

AF:

0.399

Gnomad4 OTH

AF:

0.389

Alfa

AF:

0.385

Hom.:

1840

Bravo

AF:

0.380

Asia WGS

AF:

0.347

AC:

1203

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

9.4

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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

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