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GeneBe

rs10488631

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 0.0902 in 152,324 control chromosomes in the GnomAD database, including 860 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 0.090 ( 860 hom., cov: 33)
Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436
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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 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:
0.0903
AC:
13741
AN:
152200
Hom.:
863
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0244
Gnomad AMI
AF:
0.0373
Gnomad AMR
AF:
0.138
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.00192
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.145
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.112
Gnomad OTH
AF:
0.102
GnomAD4 exome
AF:
0.333
AC:
2
AN:
6
Hom.:
0
AF XY:
0.333
AC XY:
2
AN XY:
6
show subpopulations
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.500
GnomAD4 genome
AF:
0.0902
AC:
13736
AN:
152318
Hom.:
860
Cov.:
33
AF XY:
0.0929
AC XY:
6918
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0244
Gnomad4 AMR
AF:
0.138
Gnomad4 ASJ
AF:
0.114
Gnomad4 EAS
AF:
0.00193
Gnomad4 SAS
AF:
0.153
Gnomad4 FIN
AF:
0.145
Gnomad4 NFE
AF:
0.112
Gnomad4 OTH
AF:
0.101
Alfa
AF:
0.107
Hom.:
2082
Bravo
AF:
0.0868
Asia WGS
AF:
0.0590
AC:
204
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
5.8
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: rs10488631; hg19: chr7-128594183; API