rs1992662

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 0.303 in 151,922 control chromosomes in the GnomAD database, including 7,830 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 0.30 ( 7830 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.536
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.303
AC:
46013
AN:
151802
Hom.:
7831
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.191
Gnomad AMI
AF:
0.204
Gnomad AMR
AF:
0.310
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.735
Gnomad SAS
AF:
0.453
Gnomad FIN
AF:
0.391
Gnomad MID
AF:
0.261
Gnomad NFE
AF:
0.315
Gnomad OTH
AF:
0.306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.303
AC:
46026
AN:
151922
Hom.:
7830
Cov.:
31
AF XY:
0.311
AC XY:
23054
AN XY:
74224
show subpopulations
Gnomad4 AFR
AF:
0.191
Gnomad4 AMR
AF:
0.310
Gnomad4 ASJ
AF:
0.288
Gnomad4 EAS
AF:
0.735
Gnomad4 SAS
AF:
0.453
Gnomad4 FIN
AF:
0.391
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.303
Alfa
AF:
0.301
Hom.:
2171
Bravo
AF:
0.290
Asia WGS
AF:
0.537
AC:
1867
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.7
DANN
Benign
0.52

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: rs1992662; hg19: chr5-40393852; API