rs6547853

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 0.348 in 152,022 control chromosomes in the GnomAD database, including 9,739 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 0.35 ( 9739 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.821
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 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:
0.348
AC:
52866
AN:
151904
Hom.:
9730
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.380
Gnomad AMI
AF:
0.374
Gnomad AMR
AF:
0.268
Gnomad ASJ
AF:
0.377
Gnomad EAS
AF:
0.0110
Gnomad SAS
AF:
0.179
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.384
Gnomad OTH
AF:
0.334
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.348
AC:
52897
AN:
152022
Hom.:
9739
Cov.:
32
AF XY:
0.338
AC XY:
25155
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.380
Gnomad4 AMR
AF:
0.268
Gnomad4 ASJ
AF:
0.377
Gnomad4 EAS
AF:
0.0106
Gnomad4 SAS
AF:
0.179
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.384
Gnomad4 OTH
AF:
0.330
Alfa
AF:
0.368
Hom.:
14126
Bravo
AF:
0.342
Asia WGS
AF:
0.129
AC:
451
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.8
DANN
Benign
0.55

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: rs6547853; hg19: chr2-28646801; API