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GeneBe

rs2069762

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 0.248 in 151794 control chromosomes in the gnomAD Genomes database, including 5671 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 0.25 ( 5671 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Links

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 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:
0.248
AC:
37699
AN:
151794
Hom.:
5671
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0736
Gnomad AMI
AF:
0.346
Gnomad AMR
AF:
0.298
Gnomad ASJ
AF:
0.430
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.504
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.297
GnomAD4 exome
AF:
0.328
AC:
4903
AN:
14926
Hom.:
874
AF XY:
0.331
AC XY:
2429
AN XY:
7336
show subpopulations
Gnomad4 AFR exome
AF:
0.0876
Gnomad4 AMR exome
AF:
0.318
Gnomad4 ASJ exome
AF:
0.452
Gnomad4 EAS exome
AF:
0.375
Gnomad4 SAS exome
AF:
0.515
Gnomad4 FIN exome
AF:
0.343
Gnomad4 NFE exome
AF:
0.317
Gnomad4 OTH exome
AF:
0.330
Alfa
AF:
0.286
Hom.:
3236
Bravo
AF:
0.237
Asia WGS
AF:
0.422
AC:
1467
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
Cadd
Benign
19
Dann
Benign
0.67

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: rs2069762; hg19: chr4-123377980; API