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GeneBe

rs3024505

chr1-206766559-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 0.113 in 152098 control chromosomes in the gnomAD Genomes database, including 1196 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 0.11 ( 1196 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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:
0.113
AC:
17116
AN:
152098
Hom.:
1196
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0461
Gnomad AMI
AF:
0.112
Gnomad AMR
AF:
0.0816
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.0254
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.167
Gnomad MID
AF:
0.137
Gnomad NFE
AF:
0.157
Gnomad OTH
AF:
0.123
Alfa
AF:
0.144
Hom.:
3275
Bravo
AF:
0.103
Asia WGS
AF:
0.0570
AC:
198
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
2.9
Dann
Benign
0.59

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: rs3024505; hg19: chr1-206939904;