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GeneBe

rs16944

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 0.573 in 152,000 control chromosomes in the GnomAD database, including 25,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.57 ( 25795 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.560
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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:
0.574
AC:
87133
AN:
151882
Hom.:
25788
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.456
Gnomad AMI
AF:
0.736
Gnomad AMR
AF:
0.500
Gnomad ASJ
AF:
0.651
Gnomad EAS
AF:
0.537
Gnomad SAS
AF:
0.406
Gnomad FIN
AF:
0.597
Gnomad MID
AF:
0.653
Gnomad NFE
AF:
0.666
Gnomad OTH
AF:
0.587
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.573
AC:
87156
AN:
152000
Hom.:
25795
Cov.:
32
AF XY:
0.566
AC XY:
42063
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.456
Gnomad4 AMR
AF:
0.499
Gnomad4 ASJ
AF:
0.651
Gnomad4 EAS
AF:
0.537
Gnomad4 SAS
AF:
0.405
Gnomad4 FIN
AF:
0.597
Gnomad4 NFE
AF:
0.666
Gnomad4 OTH
AF:
0.582
Alfa
AF:
0.643
Hom.:
37635
Bravo
AF:
0.564
Asia WGS
AF:
0.456
AC:
1587
AN:
3478

ClinVar

Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Antisynthetase syndrome Other:1
association, no assertion criteria providedcase-controlHLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio VillegasFeb 11, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
0.38
Dann
Benign
0.44

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: rs16944; hg19: chr2-113594867; API