chr4-99792608-G-C

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 0.331 in 151,948 control chromosomes in the GnomAD database, including 8,584 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 0.33 ( 8584 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33
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 (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.331
AC:
50305
AN:
151832
Hom.:
8566
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.277
Gnomad AMI
AF:
0.355
Gnomad AMR
AF:
0.387
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.392
Gnomad SAS
AF:
0.206
Gnomad FIN
AF:
0.264
Gnomad MID
AF:
0.382
Gnomad NFE
AF:
0.361
Gnomad OTH
AF:
0.374
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.331
AC:
50368
AN:
151948
Hom.:
8584
Cov.:
31
AF XY:
0.327
AC XY:
24291
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.278
Gnomad4 AMR
AF:
0.387
Gnomad4 ASJ
AF:
0.400
Gnomad4 EAS
AF:
0.393
Gnomad4 SAS
AF:
0.206
Gnomad4 FIN
AF:
0.264
Gnomad4 NFE
AF:
0.361
Gnomad4 OTH
AF:
0.376
Alfa
AF:
0.338
Hom.:
1084
Bravo
AF:
0.341
Asia WGS
AF:
0.292
AC:
1016
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
0.17
DANN
Benign
0.45

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: rs11735070; hg19: chr4-100713765; API