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GeneBe

rs10995190

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 0.154 in 152,140 control chromosomes in the GnomAD database, including 1,887 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 0.15 ( 1887 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.209
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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 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:
0.154
AC:
23388
AN:
152022
Hom.:
1882
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.174
Gnomad AMI
AF:
0.125
Gnomad AMR
AF:
0.116
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.0219
Gnomad SAS
AF:
0.0855
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.155
Gnomad OTH
AF:
0.153
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.154
AC:
23404
AN:
152140
Hom.:
1887
Cov.:
32
AF XY:
0.155
AC XY:
11494
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.174
Gnomad4 AMR
AF:
0.115
Gnomad4 ASJ
AF:
0.154
Gnomad4 EAS
AF:
0.0220
Gnomad4 SAS
AF:
0.0855
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.155
Gnomad4 OTH
AF:
0.151
Alfa
AF:
0.147
Hom.:
2764
Bravo
AF:
0.147
Asia WGS
AF:
0.0610
AC:
215
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
8.8
Dann
Benign
0.65

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: rs10995190; hg19: chr10-64278682; COSMIC: COSV67920557; COSMIC: COSV67920557; API