rs2967001

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 0.325 in 150,000 control chromosomes in the GnomAD database, including 8,507 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 0.33 ( 8507 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.107
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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 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:
0.325
AC:
48745
AN:
149894
Hom.:
8510
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.224
Gnomad AMI
AF:
0.350
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.308
Gnomad EAS
AF:
0.0924
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.354
Gnomad MID
AF:
0.312
Gnomad NFE
AF:
0.375
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.325
AC:
48762
AN:
150000
Hom.:
8507
Cov.:
32
AF XY:
0.325
AC XY:
23808
AN XY:
73354
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.432
Gnomad4 ASJ
AF:
0.308
Gnomad4 EAS
AF:
0.0920
Gnomad4 SAS
AF:
0.313
Gnomad4 FIN
AF:
0.354
Gnomad4 NFE
AF:
0.375
Gnomad4 OTH
AF:
0.307
Alfa
AF:
0.363
Hom.:
1650
Bravo
AF:
0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.2
DANN
Benign
0.44

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: rs2967001; hg19: chr5-19386243; API