rs12537998

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 0.307 in 152,010 control chromosomes in the GnomAD database, including 8,930 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 0.31 ( 8930 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95
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 (EAS) allele frequency at 95% confidence interval = 0.65 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:
0.308
AC:
46708
AN:
151892
Hom.:
8923
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0877
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.446
Gnomad ASJ
AF:
0.315
Gnomad EAS
AF:
0.668
Gnomad SAS
AF:
0.352
Gnomad FIN
AF:
0.399
Gnomad MID
AF:
0.287
Gnomad NFE
AF:
0.365
Gnomad OTH
AF:
0.312
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.307
AC:
46727
AN:
152010
Hom.:
8930
Cov.:
32
AF XY:
0.314
AC XY:
23364
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.0875
Gnomad4 AMR
AF:
0.446
Gnomad4 ASJ
AF:
0.315
Gnomad4 EAS
AF:
0.668
Gnomad4 SAS
AF:
0.353
Gnomad4 FIN
AF:
0.399
Gnomad4 NFE
AF:
0.365
Gnomad4 OTH
AF:
0.318
Alfa
AF:
0.346
Hom.:
9339
Bravo
AF:
0.304
Asia WGS
AF:
0.493
AC:
1716
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
0.017
DANN
Benign
0.62

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: rs12537998; hg19: chr7-127911408; API