rs36212119

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 0.0523 in 152,258 control chromosomes in the GnomAD database, including 266 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 0.052 ( 266 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.645
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 (NFE) allele frequency at 95% confidence interval = 0.0752 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:
0.0524
AC:
7970
AN:
152140
Hom.:
266
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0152
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.0605
Gnomad ASJ
AF:
0.0501
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.0155
Gnomad FIN
AF:
0.0617
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0769
Gnomad OTH
AF:
0.0650
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0523
AC:
7965
AN:
152258
Hom.:
266
Cov.:
31
AF XY:
0.0501
AC XY:
3731
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0151
Gnomad4 AMR
AF:
0.0603
Gnomad4 ASJ
AF:
0.0501
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.0153
Gnomad4 FIN
AF:
0.0617
Gnomad4 NFE
AF:
0.0769
Gnomad4 OTH
AF:
0.0639
Alfa
AF:
0.0659
Hom.:
68
Bravo
AF:
0.0512
Asia WGS
AF:
0.0110
AC:
38
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
3.6
DANN
Benign
0.51

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: rs36212119; hg19: chr1-32757253; COSMIC: COSV65190714; API