rs12557549

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0121 in 110,785 control chromosomes in the GnomAD database, including 8 homozygotes. There are 375 hemizygotes in GnomAD. 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 0.012 ( 8 hom., 375 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00
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=-0.9).
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0121 (1345/110785) while in subpopulation AMR AF= 0.02 (208/10388). AF 95% confidence interval is 0.0178. There are 8 homozygotes in gnomad4. There are 375 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0122
AC:
1348
AN:
110733
Hom.:
8
Cov.:
22
AF XY:
0.0114
AC XY:
375
AN XY:
33035
show subpopulations
Gnomad AFR
AF:
0.00227
Gnomad AMI
AF:
0.00730
Gnomad AMR
AF:
0.0201
Gnomad ASJ
AF:
0.0110
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00348
Gnomad FIN
AF:
0.00202
Gnomad MID
AF:
0.0417
Gnomad NFE
AF:
0.0184
Gnomad OTH
AF:
0.0208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0121
AC:
1345
AN:
110785
Hom.:
8
Cov.:
22
AF XY:
0.0113
AC XY:
375
AN XY:
33097
show subpopulations
Gnomad4 AFR
AF:
0.00226
Gnomad4 AMR
AF:
0.0200
Gnomad4 ASJ
AF:
0.0110
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00350
Gnomad4 FIN
AF:
0.00202
Gnomad4 NFE
AF:
0.0184
Gnomad4 OTH
AF:
0.0199
Alfa
AF:
0.0150
Hom.:
97
Bravo
AF:
0.0142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.12
DANN
Benign
0.50

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: rs12557549; hg19: chrX-66743565; API