2-44099784-A-G

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 0.586 in 151,880 control chromosomes in the GnomAD database, including 26,144 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 0.59 ( 26144 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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:
0.586
AC:
88901
AN:
151758
Hom.:
26130
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.597
Gnomad AMI
AF:
0.602
Gnomad AMR
AF:
0.668
Gnomad ASJ
AF:
0.456
Gnomad EAS
AF:
0.700
Gnomad SAS
AF:
0.557
Gnomad FIN
AF:
0.598
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.559
Gnomad OTH
AF:
0.576
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.586
AC:
88955
AN:
151880
Hom.:
26144
Cov.:
31
AF XY:
0.589
AC XY:
43676
AN XY:
74196
show subpopulations
Gnomad4 AFR
AF:
0.597
Gnomad4 AMR
AF:
0.669
Gnomad4 ASJ
AF:
0.456
Gnomad4 EAS
AF:
0.699
Gnomad4 SAS
AF:
0.556
Gnomad4 FIN
AF:
0.598
Gnomad4 NFE
AF:
0.559
Gnomad4 OTH
AF:
0.569
Alfa
AF:
0.557
Hom.:
47600
Bravo
AF:
0.593
Asia WGS
AF:
0.564
AC:
1962
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.43
DANN
Benign
0.53

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: rs2333825; hg19: chr2-44326923; API