2-85582866-C-T

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 0.514 in 152,076 control chromosomes in the GnomAD database, including 21,120 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 0.51 ( 21120 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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:
0.513
AC:
78027
AN:
151958
Hom.:
21083
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.691
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.419
Gnomad ASJ
AF:
0.401
Gnomad EAS
AF:
0.393
Gnomad SAS
AF:
0.390
Gnomad FIN
AF:
0.457
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.461
Gnomad OTH
AF:
0.496
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.514
AC:
78119
AN:
152076
Hom.:
21120
Cov.:
32
AF XY:
0.509
AC XY:
37857
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.691
Gnomad4 AMR
AF:
0.418
Gnomad4 ASJ
AF:
0.401
Gnomad4 EAS
AF:
0.392
Gnomad4 SAS
AF:
0.391
Gnomad4 FIN
AF:
0.457
Gnomad4 NFE
AF:
0.461
Gnomad4 OTH
AF:
0.498
Alfa
AF:
0.462
Hom.:
23113
Bravo
AF:
0.518
Asia WGS
AF:
0.442
AC:
1537
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.9
DANN
Benign
0.50

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: rs1561198; hg19: chr2-85809989; API