2-42758663-T-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 0.656 in 152,056 control chromosomes in the GnomAD database, including 33,891 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 0.66 ( 33891 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.432
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 (AFR) allele frequency at 95% confidence interval = 0.813 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:
0.656
AC:
99678
AN:
151938
Hom.:
33835
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.820
Gnomad AMI
AF:
0.491
Gnomad AMR
AF:
0.695
Gnomad ASJ
AF:
0.631
Gnomad EAS
AF:
0.802
Gnomad SAS
AF:
0.729
Gnomad FIN
AF:
0.561
Gnomad MID
AF:
0.665
Gnomad NFE
AF:
0.549
Gnomad OTH
AF:
0.653
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.656
AC:
99796
AN:
152056
Hom.:
33891
Cov.:
31
AF XY:
0.658
AC XY:
48930
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.820
Gnomad4 AMR
AF:
0.695
Gnomad4 ASJ
AF:
0.631
Gnomad4 EAS
AF:
0.802
Gnomad4 SAS
AF:
0.729
Gnomad4 FIN
AF:
0.561
Gnomad4 NFE
AF:
0.549
Gnomad4 OTH
AF:
0.657
Alfa
AF:
0.554
Hom.:
17821
Bravo
AF:
0.674
Asia WGS
AF:
0.794
AC:
2759
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
8.4
DANN
Benign
0.80

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: rs6719977; hg19: chr2-42985803; API