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GeneBe

rs12728740

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 0.261 in 152,118 control chromosomes in the GnomAD database, including 6,531 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 0.26 ( 6531 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.134
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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:
0.261
AC:
39634
AN:
152000
Hom.:
6530
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0687
Gnomad AMI
AF:
0.355
Gnomad AMR
AF:
0.332
Gnomad ASJ
AF:
0.304
Gnomad EAS
AF:
0.0582
Gnomad SAS
AF:
0.281
Gnomad FIN
AF:
0.459
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.342
Gnomad OTH
AF:
0.265
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.261
AC:
39648
AN:
152118
Hom.:
6531
Cov.:
32
AF XY:
0.267
AC XY:
19867
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.0686
Gnomad4 AMR
AF:
0.332
Gnomad4 ASJ
AF:
0.304
Gnomad4 EAS
AF:
0.0582
Gnomad4 SAS
AF:
0.282
Gnomad4 FIN
AF:
0.459
Gnomad4 NFE
AF:
0.342
Gnomad4 OTH
AF:
0.265
Alfa
AF:
0.316
Hom.:
7338
Bravo
AF:
0.244
Asia WGS
AF:
0.176
AC:
612
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
4.0
Dann
Benign
0.77

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: rs12728740; hg19: chr1-159710093; API