rs1369330

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 0.393 in 152,034 control chromosomes in the GnomAD database, including 13,101 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 0.39 ( 13101 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.825
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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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:
0.394
AC:
59785
AN:
151916
Hom.:
13102
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.194
Gnomad AMI
AF:
0.533
Gnomad AMR
AF:
0.443
Gnomad ASJ
AF:
0.480
Gnomad EAS
AF:
0.392
Gnomad SAS
AF:
0.353
Gnomad FIN
AF:
0.469
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.488
Gnomad OTH
AF:
0.414
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.393
AC:
59808
AN:
152034
Hom.:
13101
Cov.:
32
AF XY:
0.392
AC XY:
29148
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.194
Gnomad4 AMR
AF:
0.443
Gnomad4 ASJ
AF:
0.480
Gnomad4 EAS
AF:
0.392
Gnomad4 SAS
AF:
0.352
Gnomad4 FIN
AF:
0.469
Gnomad4 NFE
AF:
0.488
Gnomad4 OTH
AF:
0.417
Alfa
AF:
0.430
Hom.:
1830
Bravo
AF:
0.386
Asia WGS
AF:
0.423
AC:
1469
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.20
DANN
Benign
0.62

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: rs1369330; hg19: chr2-221842692; API