rs2633580

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 0.241 in 151,918 control chromosomes in the GnomAD database, including 8,008 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 ( 8008 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.657
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.241
AC:
36588
AN:
151800
Hom.:
7970
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.573
Gnomad AMI
AF:
0.0461
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.103
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.179
Gnomad FIN
AF:
0.0666
Gnomad MID
AF:
0.174
Gnomad NFE
AF:
0.0791
Gnomad OTH
AF:
0.221
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.241
AC:
36675
AN:
151918
Hom.:
8008
Cov.:
31
AF XY:
0.240
AC XY:
17806
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.574
Gnomad4 AMR
AF:
0.251
Gnomad4 ASJ
AF:
0.103
Gnomad4 EAS
AF:
0.244
Gnomad4 SAS
AF:
0.179
Gnomad4 FIN
AF:
0.0666
Gnomad4 NFE
AF:
0.0791
Gnomad4 OTH
AF:
0.219
Alfa
AF:
0.174
Hom.:
602
Bravo
AF:
0.275
Asia WGS
AF:
0.216
AC:
750
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.7
DANN
Benign
0.43

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: rs2633580; hg19: chr3-112219753; API