2-624034-G-C

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 0.851 in 152,136 control chromosomes in the GnomAD database, including 55,129 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 0.85 ( 55129 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.533
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 (EAS) allele frequency at 95% confidence interval = 0.897 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:
0.851
AC:
129298
AN:
152018
Hom.:
55084
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.887
Gnomad AMI
AF:
0.821
Gnomad AMR
AF:
0.872
Gnomad ASJ
AF:
0.745
Gnomad EAS
AF:
0.919
Gnomad SAS
AF:
0.804
Gnomad FIN
AF:
0.849
Gnomad MID
AF:
0.842
Gnomad NFE
AF:
0.828
Gnomad OTH
AF:
0.845
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.851
AC:
129399
AN:
152136
Hom.:
55129
Cov.:
32
AF XY:
0.852
AC XY:
63352
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.887
Gnomad4 AMR
AF:
0.872
Gnomad4 ASJ
AF:
0.745
Gnomad4 EAS
AF:
0.919
Gnomad4 SAS
AF:
0.802
Gnomad4 FIN
AF:
0.849
Gnomad4 NFE
AF:
0.828
Gnomad4 OTH
AF:
0.847
Alfa
AF:
0.838
Hom.:
6230
Bravo
AF:
0.854
Asia WGS
AF:
0.871
AC:
3032
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.2
DANN
Benign
0.76

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: rs6711012; hg19: chr2-624034; API