rs2498786

Variant summary

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

The variant allele was found at a frequency of 0.498 in 151,996 control chromosomes in the GnomAD database, including 20,385 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 ( 20385 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.72
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.498
AC:
75628
AN:
151876
Hom.:
20375
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.310
Gnomad AMI
AF:
0.615
Gnomad AMR
AF:
0.508
Gnomad ASJ
AF:
0.618
Gnomad EAS
AF:
0.209
Gnomad SAS
AF:
0.408
Gnomad FIN
AF:
0.623
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.610
Gnomad OTH
AF:
0.527
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.498
AC:
75657
AN:
151996
Hom.:
20385
Cov.:
32
AF XY:
0.495
AC XY:
36803
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.309
Gnomad4 AMR
AF:
0.509
Gnomad4 ASJ
AF:
0.618
Gnomad4 EAS
AF:
0.210
Gnomad4 SAS
AF:
0.409
Gnomad4 FIN
AF:
0.623
Gnomad4 NFE
AF:
0.610
Gnomad4 OTH
AF:
0.522
Alfa
AF:
0.446
Hom.:
1418
Bravo
AF:
0.481
Asia WGS
AF:
0.311
AC:
1085
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
5.4
DANN
Benign
0.56

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.

Other links and lift over

dbSNP: rs2498786; hg19: chr14-105262368; API