rs1977719

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 ( 10067 hom., 9398 hem., cov: 16)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.999
Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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:
0.496
AC:
47281
AN:
95328
Hom.:
10073
Cov.:
16
AF XY:
0.435
AC XY:
9393
AN XY:
21612
show subpopulations
Gnomad AFR
AF:
0.413
Gnomad AMI
AF:
0.568
Gnomad AMR
AF:
0.396
Gnomad ASJ
AF:
0.488
Gnomad EAS
AF:
0.393
Gnomad SAS
AF:
0.515
Gnomad FIN
AF:
0.402
Gnomad MID
AF:
0.492
Gnomad NFE
AF:
0.571
Gnomad OTH
AF:
0.492
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.496
AC:
47273
AN:
95332
Hom.:
10067
Cov.:
16
AF XY:
0.434
AC XY:
9398
AN XY:
21630
show subpopulations
Gnomad4 AFR
AF:
0.413
Gnomad4 AMR
AF:
0.396
Gnomad4 ASJ
AF:
0.488
Gnomad4 EAS
AF:
0.393
Gnomad4 SAS
AF:
0.514
Gnomad4 FIN
AF:
0.402
Gnomad4 NFE
AF:
0.571
Gnomad4 OTH
AF:
0.492
Alfa
AF:
0.545
Hom.:
3512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.12
DANN
Benign
0.22

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: rs1977719; hg19: chrX-78397143; API