5-25841504-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 0.295 in 151,778 control chromosomes in the GnomAD database, including 7,087 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 0.30 ( 7087 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.212
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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:
0.295
AC:
44815
AN:
151660
Hom.:
7085
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.179
Gnomad AMI
AF:
0.321
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.427
Gnomad EAS
AF:
0.254
Gnomad SAS
AF:
0.341
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.352
Gnomad OTH
AF:
0.312
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.295
AC:
44841
AN:
151778
Hom.:
7087
Cov.:
32
AF XY:
0.298
AC XY:
22129
AN XY:
74152
show subpopulations
Gnomad4 AFR
AF:
0.179
Gnomad4 AMR
AF:
0.287
Gnomad4 ASJ
AF:
0.427
Gnomad4 EAS
AF:
0.255
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.352
Gnomad4 OTH
AF:
0.314
Alfa
AF:
0.349
Hom.:
16058
Bravo
AF:
0.285
Asia WGS
AF:
0.286
AC:
993
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
5.0
DANN
Benign
0.41

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: rs396045; hg19: chr5-25841613; API