rs4908736

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 0.219 in 151,752 control chromosomes in the GnomAD database, including 5,504 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 0.22 ( 5504 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104
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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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:
0.219
AC:
33177
AN:
151638
Hom.:
5486
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.308
Gnomad AMI
AF:
0.131
Gnomad AMR
AF:
0.357
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.695
Gnomad SAS
AF:
0.251
Gnomad FIN
AF:
0.0824
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.123
Gnomad OTH
AF:
0.213
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33240
AN:
151752
Hom.:
5504
Cov.:
33
AF XY:
0.225
AC XY:
16673
AN XY:
74214
show subpopulations
Gnomad4 AFR
AF:
0.308
Gnomad4 AMR
AF:
0.358
Gnomad4 ASJ
AF:
0.124
Gnomad4 EAS
AF:
0.695
Gnomad4 SAS
AF:
0.251
Gnomad4 FIN
AF:
0.0824
Gnomad4 NFE
AF:
0.123
Gnomad4 OTH
AF:
0.216
Alfa
AF:
0.146
Hom.:
4944
Bravo
AF:
0.246
Asia WGS
AF:
0.448
AC:
1555
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.84
DANN
Benign
0.35

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: rs4908736; hg19: chr1-8187211; API