chr7-54890765-G-A

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 0.254 in 151,962 control chromosomes in the GnomAD database, including 5,351 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 0.25 ( 5351 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0500
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 (NFE) allele frequency at 95% confidence interval = 0.307 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:
0.255
AC:
38675
AN:
151844
Hom.:
5353
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.442
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.0199
Gnomad SAS
AF:
0.177
Gnomad FIN
AF:
0.243
Gnomad MID
AF:
0.369
Gnomad NFE
AF:
0.311
Gnomad OTH
AF:
0.290
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.254
AC:
38669
AN:
151962
Hom.:
5351
Cov.:
33
AF XY:
0.248
AC XY:
18394
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.0199
Gnomad4 SAS
AF:
0.177
Gnomad4 FIN
AF:
0.243
Gnomad4 NFE
AF:
0.311
Gnomad4 OTH
AF:
0.287
Alfa
AF:
0.308
Hom.:
8884
Bravo
AF:
0.251
Asia WGS
AF:
0.0860
AC:
297
AN:
3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.1
DANN
Benign
0.25

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: rs6945082; hg19: chr7-54958458; API