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GeneBe

rs2965140

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 0.127 in 144,236 control chromosomes in the GnomAD database, including 2,662 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 0.13 ( 2662 hom., cov: 27)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39
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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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:
0.126
AC:
18233
AN:
144142
Hom.:
2635
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.363
Gnomad AMI
AF:
0.0397
Gnomad AMR
AF:
0.0693
Gnomad ASJ
AF:
0.0488
Gnomad EAS
AF:
0.0594
Gnomad SAS
AF:
0.130
Gnomad FIN
AF:
0.00236
Gnomad MID
AF:
0.0846
Gnomad NFE
AF:
0.0261
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.127
AC:
18308
AN:
144236
Hom.:
2662
Cov.:
27
AF XY:
0.127
AC XY:
8799
AN XY:
69414
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.0691
Gnomad4 ASJ
AF:
0.0488
Gnomad4 EAS
AF:
0.0596
Gnomad4 SAS
AF:
0.130
Gnomad4 FIN
AF:
0.00236
Gnomad4 NFE
AF:
0.0261
Gnomad4 OTH
AF:
0.107
Alfa
AF:
0.0816
Hom.:
209
Bravo
AF:
0.137
Asia WGS
AF:
0.125
AC:
435
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
1.4
Dann
Benign
0.088

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: rs2965140; hg19: chr19-45275393; API