rs4757610

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 0.433 in 151,962 control chromosomes in the GnomAD database, including 14,796 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 0.43 ( 14796 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.66
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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:
0.433
AC:
65718
AN:
151844
Hom.:
14781
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.537
Gnomad AMI
AF:
0.426
Gnomad AMR
AF:
0.357
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.225
Gnomad SAS
AF:
0.342
Gnomad FIN
AF:
0.386
Gnomad MID
AF:
0.468
Gnomad NFE
AF:
0.421
Gnomad OTH
AF:
0.437
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.433
AC:
65784
AN:
151962
Hom.:
14796
Cov.:
32
AF XY:
0.425
AC XY:
31574
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.538
Gnomad4 AMR
AF:
0.357
Gnomad4 ASJ
AF:
0.316
Gnomad4 EAS
AF:
0.224
Gnomad4 SAS
AF:
0.342
Gnomad4 FIN
AF:
0.386
Gnomad4 NFE
AF:
0.421
Gnomad4 OTH
AF:
0.436
Alfa
AF:
0.421
Hom.:
1727
Bravo
AF:
0.436
Asia WGS
AF:
0.306
AC:
1069
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.0
DANN
Benign
0.53

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: rs4757610; hg19: chr11-18069421; API