4-99406180-T-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 0.358 in 147,932 control chromosomes in the GnomAD database, including 9,715 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 0.36 ( 9715 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.932
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 (EAS) allele frequency at 95% confidence interval = 0.601 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:
0.358
AC:
52891
AN:
147850
Hom.:
9711
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.306
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.300
Gnomad EAS
AF:
0.619
Gnomad SAS
AF:
0.509
Gnomad FIN
AF:
0.359
Gnomad MID
AF:
0.437
Gnomad NFE
AF:
0.387
Gnomad OTH
AF:
0.356
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.358
AC:
52924
AN:
147932
Hom.:
9715
Cov.:
30
AF XY:
0.361
AC XY:
25961
AN XY:
71974
show subpopulations
Gnomad4 AFR
AF:
0.276
Gnomad4 AMR
AF:
0.320
Gnomad4 ASJ
AF:
0.300
Gnomad4 EAS
AF:
0.619
Gnomad4 SAS
AF:
0.509
Gnomad4 FIN
AF:
0.359
Gnomad4 NFE
AF:
0.387
Gnomad4 OTH
AF:
0.357
Alfa
AF:
0.214
Hom.:
502
Bravo
AF:
0.343
Asia WGS
AF:
0.448
AC:
1556
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
5.1
DANN
Benign
0.28

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: rs2083687; hg19: chr4-100327337; API