rs994014

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 0.421 in 151,818 control chromosomes in the GnomAD database, including 16,145 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 0.42 ( 16145 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.166
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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:
0.420
AC:
63783
AN:
151700
Hom.:
16107
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.716
Gnomad AMI
AF:
0.318
Gnomad AMR
AF:
0.314
Gnomad ASJ
AF:
0.283
Gnomad EAS
AF:
0.183
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.363
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.317
Gnomad OTH
AF:
0.359
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.421
AC:
63885
AN:
151818
Hom.:
16145
Cov.:
31
AF XY:
0.415
AC XY:
30797
AN XY:
74212
show subpopulations
Gnomad4 AFR
AF:
0.716
Gnomad4 AMR
AF:
0.314
Gnomad4 ASJ
AF:
0.283
Gnomad4 EAS
AF:
0.184
Gnomad4 SAS
AF:
0.215
Gnomad4 FIN
AF:
0.363
Gnomad4 NFE
AF:
0.317
Gnomad4 OTH
AF:
0.357
Alfa
AF:
0.321
Hom.:
11204
Bravo
AF:
0.430
Asia WGS
AF:
0.230
AC:
802
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
4.2
DANN
Benign
0.71

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: rs994014; hg19: chr4-82165790; API