rs10981955

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 0.0291 in 152,062 control chromosomes in the GnomAD database, including 91 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 0.029 ( 91 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.671
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=-1.0).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0291 (4431/152062) while in subpopulation NFE AF= 0.0456 (3101/67968). AF 95% confidence interval is 0.0443. There are 91 homozygotes in gnomad4. There are 2093 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 91 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:
0.0292
AC:
4432
AN:
151944
Hom.:
91
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00870
Gnomad AMI
AF:
0.0198
Gnomad AMR
AF:
0.0243
Gnomad ASJ
AF:
0.0107
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0133
Gnomad FIN
AF:
0.0396
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0456
Gnomad OTH
AF:
0.0268
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0291
AC:
4431
AN:
152062
Hom.:
91
Cov.:
32
AF XY:
0.0282
AC XY:
2093
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.00868
Gnomad4 AMR
AF:
0.0243
Gnomad4 ASJ
AF:
0.0107
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0133
Gnomad4 FIN
AF:
0.0396
Gnomad4 NFE
AF:
0.0456
Gnomad4 OTH
AF:
0.0265
Alfa
AF:
0.0395
Hom.:
178
Bravo
AF:
0.0273
Asia WGS
AF:
0.00897
AC:
32
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.37
DANN
Benign
0.59

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: rs10981955; hg19: chr9-116591472; API