4-109907647-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 0.151 in 152,206 control chromosomes in the GnomAD database, including 3,003 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 0.15 ( 3003 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.502
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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:
0.151
AC:
22928
AN:
152088
Hom.:
2990
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.347
Gnomad AMI
AF:
0.165
Gnomad AMR
AF:
0.116
Gnomad ASJ
AF:
0.108
Gnomad EAS
AF:
0.203
Gnomad SAS
AF:
0.0878
Gnomad FIN
AF:
0.0455
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0590
Gnomad OTH
AF:
0.132
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22982
AN:
152206
Hom.:
3003
Cov.:
33
AF XY:
0.150
AC XY:
11169
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.348
Gnomad4 AMR
AF:
0.115
Gnomad4 ASJ
AF:
0.108
Gnomad4 EAS
AF:
0.202
Gnomad4 SAS
AF:
0.0883
Gnomad4 FIN
AF:
0.0455
Gnomad4 NFE
AF:
0.0590
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.121
Hom.:
299
Bravo
AF:
0.165
Asia WGS
AF:
0.147
AC:
512
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.2
DANN
Benign
0.71

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: rs6533477; hg19: chr4-110828803; API