rs4886410

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 0.434 in 151,944 control chromosomes in the GnomAD database, including 18,739 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 ( 18739 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.120
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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:
0.435
AC:
66039
AN:
151826
Hom.:
18746
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.117
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.358
Gnomad ASJ
AF:
0.560
Gnomad EAS
AF:
0.174
Gnomad SAS
AF:
0.200
Gnomad FIN
AF:
0.551
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.657
Gnomad OTH
AF:
0.453
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.434
AC:
66016
AN:
151944
Hom.:
18739
Cov.:
31
AF XY:
0.421
AC XY:
31268
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.117
Gnomad4 AMR
AF:
0.358
Gnomad4 ASJ
AF:
0.560
Gnomad4 EAS
AF:
0.174
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.551
Gnomad4 NFE
AF:
0.657
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.533
Hom.:
3072
Bravo
AF:
0.414
Asia WGS
AF:
0.166
AC:
583
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.9
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: rs4886410; hg19: chr15-75065644; API