2-56682617-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 0.63 in 152,028 control chromosomes in the GnomAD database, including 31,358 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 0.63 ( 31358 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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:
0.630
AC:
95689
AN:
151910
Hom.:
31302
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.819
Gnomad AMI
AF:
0.307
Gnomad AMR
AF:
0.614
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.676
Gnomad SAS
AF:
0.516
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.535
Gnomad OTH
AF:
0.596
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.630
AC:
95803
AN:
152028
Hom.:
31358
Cov.:
31
AF XY:
0.635
AC XY:
47167
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.819
Gnomad4 AMR
AF:
0.614
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.676
Gnomad4 SAS
AF:
0.516
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.535
Gnomad4 OTH
AF:
0.598
Alfa
AF:
0.449
Hom.:
1154
Bravo
AF:
0.638
Asia WGS
AF:
0.607
AC:
2109
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.39
DANN
Benign
0.54

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: rs6732705; hg19: chr2-56909752; API