rs2317332

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0258 in 152,268 control chromosomes in the GnomAD database, including 80 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 0.026 ( 80 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.957
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).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0258 (3924/152268) while in subpopulation NFE AF= 0.0435 (2961/68014). AF 95% confidence interval is 0.0422. There are 80 homozygotes in gnomad4. There are 1784 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 80 gene

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:
0.0258
AC:
3925
AN:
152150
Hom.:
80
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00724
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.0170
Gnomad ASJ
AF:
0.0346
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0141
Gnomad FIN
AF:
0.0135
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0436
Gnomad OTH
AF:
0.0220
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0258
AC:
3924
AN:
152268
Hom.:
80
Cov.:
32
AF XY:
0.0240
AC XY:
1784
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.00722
Gnomad4 AMR
AF:
0.0169
Gnomad4 ASJ
AF:
0.0346
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0141
Gnomad4 FIN
AF:
0.0135
Gnomad4 NFE
AF:
0.0435
Gnomad4 OTH
AF:
0.0218
Alfa
AF:
0.0382
Hom.:
71
Bravo
AF:
0.0255
Asia WGS
AF:
0.00751
AC:
29
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
5.1
DANN
Benign
0.71

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: rs2317332; hg19: chr3-100761773; API