rs7025295

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 0.335 in 152,114 control chromosomes in the GnomAD database, including 8,982 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 0.34 ( 8982 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415
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 (NFE) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.336
AC:
50995
AN:
151996
Hom.:
8980
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.230
Gnomad AMI
AF:
0.442
Gnomad AMR
AF:
0.371
Gnomad ASJ
AF:
0.386
Gnomad EAS
AF:
0.284
Gnomad SAS
AF:
0.346
Gnomad FIN
AF:
0.423
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.377
Gnomad OTH
AF:
0.362
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.335
AC:
51009
AN:
152114
Hom.:
8982
Cov.:
32
AF XY:
0.340
AC XY:
25303
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.230
Gnomad4 AMR
AF:
0.370
Gnomad4 ASJ
AF:
0.386
Gnomad4 EAS
AF:
0.284
Gnomad4 SAS
AF:
0.347
Gnomad4 FIN
AF:
0.423
Gnomad4 NFE
AF:
0.377
Gnomad4 OTH
AF:
0.359
Alfa
AF:
0.372
Hom.:
18464
Bravo
AF:
0.326
Asia WGS
AF:
0.265
AC:
921
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.73
DANN
Benign
0.75

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: rs7025295; hg19: chr9-6395247; API