rs7547072

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 0.453 in 151,750 control chromosomes in the GnomAD database, including 16,215 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 0.45 ( 16215 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.910
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.453
AC:
68725
AN:
151628
Hom.:
16207
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.332
Gnomad AMI
AF:
0.587
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.495
Gnomad EAS
AF:
0.537
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.462
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.502
Gnomad OTH
AF:
0.452
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.453
AC:
68761
AN:
151750
Hom.:
16215
Cov.:
30
AF XY:
0.454
AC XY:
33692
AN XY:
74130
show subpopulations
Gnomad4 AFR
AF:
0.332
Gnomad4 AMR
AF:
0.501
Gnomad4 ASJ
AF:
0.495
Gnomad4 EAS
AF:
0.538
Gnomad4 SAS
AF:
0.486
Gnomad4 FIN
AF:
0.462
Gnomad4 NFE
AF:
0.502
Gnomad4 OTH
AF:
0.447
Alfa
AF:
0.491
Hom.:
20381
Bravo
AF:
0.451
Asia WGS
AF:
0.486
AC:
1692
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.39
DANN
Benign
0.40

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: rs7547072; hg19: chr1-154639255; API