rs5961738

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0151 in 110,622 control chromosomes in the GnomAD database, including 15 homozygotes. There are 495 hemizygotes in GnomAD. 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 0.015 ( 15 hom., 495 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.809
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=-0.94).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0151 (1671/110622) while in subpopulation NFE AF= 0.0215 (1140/52937). AF 95% confidence interval is 0.0205. There are 15 homozygotes in gnomad4. There are 495 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0151
AC:
1670
AN:
110575
Hom.:
15
Cov.:
23
AF XY:
0.0151
AC XY:
495
AN XY:
32851
show subpopulations
Gnomad AFR
AF:
0.00238
Gnomad AMI
AF:
0.00294
Gnomad AMR
AF:
0.0169
Gnomad ASJ
AF:
0.0168
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00679
Gnomad FIN
AF:
0.0313
Gnomad MID
AF:
0.0298
Gnomad NFE
AF:
0.0215
Gnomad OTH
AF:
0.0195
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0151
AC:
1671
AN:
110622
Hom.:
15
Cov.:
23
AF XY:
0.0150
AC XY:
495
AN XY:
32908
show subpopulations
Gnomad4 AFR
AF:
0.00241
Gnomad4 AMR
AF:
0.0169
Gnomad4 ASJ
AF:
0.0168
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00644
Gnomad4 FIN
AF:
0.0313
Gnomad4 NFE
AF:
0.0215
Gnomad4 OTH
AF:
0.0192
Alfa
AF:
0.00125
Hom.:
666
Bravo
AF:
0.0150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.91
DANN
Benign
0.90

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: rs5961738; hg19: chrX-5496093; API