5-8174936-C-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 0.59 in 152,076 control chromosomes in the GnomAD database, including 27,977 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 0.59 ( 27977 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.590
AC:
89678
AN:
151958
Hom.:
27968
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.384
Gnomad AMI
AF:
0.618
Gnomad AMR
AF:
0.616
Gnomad ASJ
AF:
0.600
Gnomad EAS
AF:
0.839
Gnomad SAS
AF:
0.631
Gnomad FIN
AF:
0.748
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.663
Gnomad OTH
AF:
0.584
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.590
AC:
89701
AN:
152076
Hom.:
27977
Cov.:
33
AF XY:
0.596
AC XY:
44293
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.383
Gnomad4 AMR
AF:
0.616
Gnomad4 ASJ
AF:
0.600
Gnomad4 EAS
AF:
0.839
Gnomad4 SAS
AF:
0.631
Gnomad4 FIN
AF:
0.748
Gnomad4 NFE
AF:
0.663
Gnomad4 OTH
AF:
0.586
Alfa
AF:
0.640
Hom.:
42247
Bravo
AF:
0.575
Asia WGS
AF:
0.688
AC:
2391
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.13
DANN
Benign
0.58

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: rs901893; hg19: chr5-8175049; API