rs7338014

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 0.322 in 151,788 control chromosomes in the GnomAD database, including 8,426 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 0.32 ( 8426 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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:
0.321
AC:
48750
AN:
151670
Hom.:
8407
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.415
Gnomad AMI
AF:
0.230
Gnomad AMR
AF:
0.339
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.469
Gnomad SAS
AF:
0.303
Gnomad FIN
AF:
0.365
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48818
AN:
151788
Hom.:
8426
Cov.:
31
AF XY:
0.328
AC XY:
24313
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.415
Gnomad4 AMR
AF:
0.338
Gnomad4 ASJ
AF:
0.288
Gnomad4 EAS
AF:
0.469
Gnomad4 SAS
AF:
0.303
Gnomad4 FIN
AF:
0.365
Gnomad4 NFE
AF:
0.248
Gnomad4 OTH
AF:
0.308
Alfa
AF:
0.269
Hom.:
2690
Bravo
AF:
0.326
Asia WGS
AF:
0.341
AC:
1185
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.1
DANN
Benign
0.46

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: rs7338014; hg19: chr13-22486015; API