rs2817611

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 0.219 in 151,976 control chromosomes in the GnomAD database, including 7,294 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 0.22 ( 7294 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.24
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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:
0.219
AC:
33309
AN:
151856
Hom.:
7277
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.571
Gnomad AMI
AF:
0.0559
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.0843
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.197
Gnomad NFE
AF:
0.0666
Gnomad OTH
AF:
0.182
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33358
AN:
151976
Hom.:
7294
Cov.:
31
AF XY:
0.219
AC XY:
16273
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.571
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.127
Gnomad4 EAS
AF:
0.0841
Gnomad4 SAS
AF:
0.233
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.0666
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.156
Hom.:
567
Bravo
AF:
0.229
Asia WGS
AF:
0.189
AC:
656
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
13
DANN
Benign
0.65

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: rs2817611; hg19: chr1-11613163; API