3-36209948-C-T

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 0.0366 in 152,182 control chromosomes in the GnomAD database, including 313 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 0.037 ( 313 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126
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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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:
0.0366
AC:
5565
AN:
152064
Hom.:
312
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.117
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0266
Gnomad ASJ
AF:
0.0109
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00559
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.00213
Gnomad OTH
AF:
0.0403
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0366
AC:
5573
AN:
152182
Hom.:
313
Cov.:
32
AF XY:
0.0359
AC XY:
2671
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.117
Gnomad4 AMR
AF:
0.0266
Gnomad4 ASJ
AF:
0.0109
Gnomad4 EAS
AF:
0.000194
Gnomad4 SAS
AF:
0.00498
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00212
Gnomad4 OTH
AF:
0.0399
Alfa
AF:
0.0170
Hom.:
32
Bravo
AF:
0.0435
Asia WGS
AF:
0.0130
AC:
44
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
4.8
DANN
Benign
0.58

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: rs10514691; hg19: chr3-36251440; API