rs3757387

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 0.377 in 151,898 control chromosomes in the GnomAD database, including 11,627 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 0.38 ( 11627 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0880
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 (NFE) allele frequency at 95% confidence interval = 0.442 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:
0.377
AC:
57274
AN:
151780
Hom.:
11629
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.457
Gnomad AMR
AF:
0.405
Gnomad ASJ
AF:
0.523
Gnomad EAS
AF:
0.122
Gnomad SAS
AF:
0.397
Gnomad FIN
AF:
0.401
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.447
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.377
AC:
57291
AN:
151898
Hom.:
11627
Cov.:
31
AF XY:
0.373
AC XY:
27673
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.260
Gnomad4 AMR
AF:
0.405
Gnomad4 ASJ
AF:
0.523
Gnomad4 EAS
AF:
0.122
Gnomad4 SAS
AF:
0.397
Gnomad4 FIN
AF:
0.401
Gnomad4 NFE
AF:
0.447
Gnomad4 OTH
AF:
0.414
Alfa
AF:
0.408
Hom.:
1633
Bravo
AF:
0.374
Asia WGS
AF:
0.238
AC:
829
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
3.4
DANN
Benign
0.61

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: rs3757387; hg19: chr7-128576086; API