rs7336303

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 0.146 in 152,150 control chromosomes in the GnomAD database, including 4,338 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 0.15 ( 4338 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28
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).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.146
AC:
22163
AN:
152032
Hom.:
4341
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.447
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0963
Gnomad ASJ
AF:
0.0109
Gnomad EAS
AF:
0.0901
Gnomad SAS
AF:
0.0425
Gnomad FIN
AF:
0.00877
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0165
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.146
AC:
22200
AN:
152150
Hom.:
4338
Cov.:
32
AF XY:
0.144
AC XY:
10688
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.0965
Gnomad4 ASJ
AF:
0.0109
Gnomad4 EAS
AF:
0.0903
Gnomad4 SAS
AF:
0.0428
Gnomad4 FIN
AF:
0.00877
Gnomad4 NFE
AF:
0.0165
Gnomad4 OTH
AF:
0.121
Alfa
AF:
0.0390
Hom.:
836
Bravo
AF:
0.166
Asia WGS
AF:
0.0920
AC:
321
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
0.57
DANN
Benign
0.49

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: rs7336303; hg19: chr13-45658934; API