chr20-19463266-G-T

Variant summary

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

The NM_020689.4(SLC24A3):​c.272-52222G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,916 control chromosomes in the GnomAD database, including 19,844 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 0.50 ( 19844 hom., cov: 32)

Consequence

SLC24A3
NM_020689.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.214
Variant links:
Genes affected
SLC24A3 (HGNC:10977): (solute carrier family 24 member 3) Plasma membrane sodium/calcium exchangers are an important component of intracellular calcium homeostasis and electrical conduction. Potassium-dependent sodium/calcium exchangers such as SLC24A3 are believed to transport 1 intracellular calcium and 1 potassium ion in exchange for 4 extracellular sodium ions (Kraev et al., 2001 [PubMed 11294880]).[supplied by OMIM, Mar 2008]

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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC24A3NM_020689.4 linkuse as main transcriptc.272-52222G>T intron_variant ENST00000328041.11 NP_065740.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC24A3ENST00000328041.11 linkuse as main transcriptc.272-52222G>T intron_variant 1 NM_020689.4 ENSP00000333519 P1

Frequencies

GnomAD3 genomes
AF:
0.500
AC:
75969
AN:
151798
Hom.:
19838
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.347
Gnomad AMI
AF:
0.457
Gnomad AMR
AF:
0.510
Gnomad ASJ
AF:
0.511
Gnomad EAS
AF:
0.516
Gnomad SAS
AF:
0.523
Gnomad FIN
AF:
0.619
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.570
Gnomad OTH
AF:
0.520
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.500
AC:
76009
AN:
151916
Hom.:
19844
Cov.:
32
AF XY:
0.503
AC XY:
37324
AN XY:
74220
show subpopulations
Gnomad4 AFR
AF:
0.347
Gnomad4 AMR
AF:
0.511
Gnomad4 ASJ
AF:
0.511
Gnomad4 EAS
AF:
0.517
Gnomad4 SAS
AF:
0.523
Gnomad4 FIN
AF:
0.619
Gnomad4 NFE
AF:
0.570
Gnomad4 OTH
AF:
0.518
Alfa
AF:
0.537
Hom.:
4261
Bravo
AF:
0.484
Asia WGS
AF:
0.488
AC:
1697
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.3
DANN
Benign
0.65

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

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

Other links and lift over

dbSNP: rs6081603; hg19: chr20-19443910; API