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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein 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
Feb 11, 2020
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas
Significance: association
Review Status: no assertion criteria provided
Collection Method: case-control

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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