4-144566782-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 0.367 in 152,058 control chromosomes in the GnomAD database, including 10,773 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 0.37 ( 10773 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.309
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.367
AC:
55805
AN:
151940
Hom.:
10765
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.394
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.362
Gnomad EAS
AF:
0.301
Gnomad SAS
AF:
0.491
Gnomad FIN
AF:
0.536
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.413
Gnomad OTH
AF:
0.340
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.367
AC:
55821
AN:
152058
Hom.:
10773
Cov.:
32
AF XY:
0.373
AC XY:
27689
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.261
Gnomad4 AMR
AF:
0.321
Gnomad4 ASJ
AF:
0.362
Gnomad4 EAS
AF:
0.301
Gnomad4 SAS
AF:
0.492
Gnomad4 FIN
AF:
0.536
Gnomad4 NFE
AF:
0.413
Gnomad4 OTH
AF:
0.339
Alfa
AF:
0.406
Hom.:
1661
Bravo
AF:
0.339
Asia WGS
AF:
0.367
AC:
1277
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.80
DANN
Benign
0.55

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: rs6537296; hg19: chr4-145487934; API