rs1368065

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 0.239 in 151,686 control chromosomes in the GnomAD database, including 4,907 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 0.24 ( 4907 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.123
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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:
0.239
AC:
36231
AN:
151568
Hom.:
4891
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.316
Gnomad AMI
AF:
0.142
Gnomad AMR
AF:
0.301
Gnomad ASJ
AF:
0.221
Gnomad EAS
AF:
0.395
Gnomad SAS
AF:
0.342
Gnomad FIN
AF:
0.0733
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.186
Gnomad OTH
AF:
0.263
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.239
AC:
36274
AN:
151686
Hom.:
4907
Cov.:
32
AF XY:
0.238
AC XY:
17663
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.316
Gnomad4 AMR
AF:
0.302
Gnomad4 ASJ
AF:
0.221
Gnomad4 EAS
AF:
0.395
Gnomad4 SAS
AF:
0.342
Gnomad4 FIN
AF:
0.0733
Gnomad4 NFE
AF:
0.186
Gnomad4 OTH
AF:
0.261
Alfa
AF:
0.207
Hom.:
877
Bravo
AF:
0.258
Asia WGS
AF:
0.335
AC:
1168
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.5
DANN
Benign
0.54

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: rs1368065; hg19: chr2-222089528; API