rs10437896

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 0.125 in 152,116 control chromosomes in the GnomAD database, including 1,889 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 ( 1889 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.427
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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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:
0.125
AC:
19011
AN:
151998
Hom.:
1878
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.254
Gnomad AMI
AF:
0.0263
Gnomad AMR
AF:
0.137
Gnomad ASJ
AF:
0.0338
Gnomad EAS
AF:
0.285
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.0524
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0477
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.125
AC:
19065
AN:
152116
Hom.:
1889
Cov.:
32
AF XY:
0.128
AC XY:
9520
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.255
Gnomad4 AMR
AF:
0.137
Gnomad4 ASJ
AF:
0.0338
Gnomad4 EAS
AF:
0.285
Gnomad4 SAS
AF:
0.154
Gnomad4 FIN
AF:
0.0524
Gnomad4 NFE
AF:
0.0477
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.0726
Hom.:
314
Bravo
AF:
0.137
Asia WGS
AF:
0.234
AC:
813
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.1
DANN
Benign
0.91

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: rs10437896; hg19: chr12-107557617; API