rs1402516

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.0431 in 152,196 control chromosomes in the GnomAD database, including 456 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 ( 456 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0431
AC:
6558
AN:
152078
Hom.:
457
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0445
Gnomad AMI
AF:
0.0592
Gnomad AMR
AF:
0.0298
Gnomad ASJ
AF:
0.0242
Gnomad EAS
AF:
0.376
Gnomad SAS
AF:
0.0480
Gnomad FIN
AF:
0.0270
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0228
Gnomad OTH
AF:
0.0435
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0431
AC:
6560
AN:
152196
Hom.:
456
Cov.:
33
AF XY:
0.0457
AC XY:
3400
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.0446
Gnomad4 AMR
AF:
0.0298
Gnomad4 ASJ
AF:
0.0242
Gnomad4 EAS
AF:
0.377
Gnomad4 SAS
AF:
0.0481
Gnomad4 FIN
AF:
0.0270
Gnomad4 NFE
AF:
0.0228
Gnomad4 OTH
AF:
0.0412
Alfa
AF:
0.0310
Hom.:
15
Bravo
AF:
0.0461
Asia WGS
AF:
0.184
AC:
638
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
CADD
Benign
17
DANN
Benign
0.58

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: rs1402516; hg19: chr14-48466535; API