5-95611429-G-T

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 0.489 in 151,982 control chromosomes in the GnomAD database, including 20,499 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 0.49 ( 20499 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.284
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 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:
0.489
AC:
74191
AN:
151864
Hom.:
20448
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.756
Gnomad AMI
AF:
0.270
Gnomad AMR
AF:
0.468
Gnomad ASJ
AF:
0.446
Gnomad EAS
AF:
0.509
Gnomad SAS
AF:
0.489
Gnomad FIN
AF:
0.286
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.365
Gnomad OTH
AF:
0.479
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.489
AC:
74305
AN:
151982
Hom.:
20499
Cov.:
32
AF XY:
0.485
AC XY:
36056
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.757
Gnomad4 AMR
AF:
0.469
Gnomad4 ASJ
AF:
0.446
Gnomad4 EAS
AF:
0.510
Gnomad4 SAS
AF:
0.489
Gnomad4 FIN
AF:
0.286
Gnomad4 NFE
AF:
0.365
Gnomad4 OTH
AF:
0.477
Alfa
AF:
0.403
Hom.:
7422
Bravo
AF:
0.511
Asia WGS
AF:
0.481
AC:
1672
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.0
DANN
Benign
0.24

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: rs956274; hg19: chr5-94947133; COSMIC: COSV60168081; API