rs2179915

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 0.132 in 151,810 control chromosomes in the GnomAD database, including 2,544 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 0.13 ( 2544 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.187
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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:
0.132
AC:
20039
AN:
151694
Hom.:
2539
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.337
Gnomad AMI
AF:
0.0417
Gnomad AMR
AF:
0.0687
Gnomad ASJ
AF:
0.0130
Gnomad EAS
AF:
0.0129
Gnomad SAS
AF:
0.0667
Gnomad FIN
AF:
0.0510
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0563
Gnomad OTH
AF:
0.120
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.132
AC:
20062
AN:
151810
Hom.:
2544
Cov.:
31
AF XY:
0.128
AC XY:
9489
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.337
Gnomad4 AMR
AF:
0.0686
Gnomad4 ASJ
AF:
0.0130
Gnomad4 EAS
AF:
0.0127
Gnomad4 SAS
AF:
0.0664
Gnomad4 FIN
AF:
0.0510
Gnomad4 NFE
AF:
0.0563
Gnomad4 OTH
AF:
0.118
Alfa
AF:
0.0746
Hom.:
520
Bravo
AF:
0.141
Asia WGS
AF:
0.0880
AC:
307
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.8
DANN
Benign
0.14

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: rs2179915; hg19: chr6-33065734; API