chr5-165337081-A-G

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 0.0956 in 152,254 control chromosomes in the GnomAD database, including 929 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 0.096 ( 929 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.366
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=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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:
0.0957
AC:
14557
AN:
152136
Hom.:
930
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0257
Gnomad AMI
AF:
0.132
Gnomad AMR
AF:
0.103
Gnomad ASJ
AF:
0.0524
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.124
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.141
Gnomad OTH
AF:
0.0738
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0956
AC:
14550
AN:
152254
Hom.:
929
Cov.:
32
AF XY:
0.0934
AC XY:
6954
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0256
Gnomad4 AMR
AF:
0.103
Gnomad4 ASJ
AF:
0.0524
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.124
Gnomad4 NFE
AF:
0.141
Gnomad4 OTH
AF:
0.0725
Alfa
AF:
0.115
Hom.:
739
Bravo
AF:
0.0905
Asia WGS
AF:
0.0400
AC:
141
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.6
DANN
Benign
0.47

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: rs1145652; hg19: chr5-164764087; API