rs914051

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000430545.4(ENSG00000237153):​n.393+13795G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,968 control chromosomes in the GnomAD database, including 14,593 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 ( 14593 hom., cov: 32)

Consequence

ENSG00000237153
ENST00000430545.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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
ENSG00000237153ENST00000430545.4 linkn.393+13795G>A intron_variant Intron 2 of 2 5
ENSG00000237153ENST00000649821.1 linkn.179+9836G>A intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.432
AC:
65616
AN:
151850
Hom.:
14566
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.489
Gnomad AMI
AF:
0.466
Gnomad AMR
AF:
0.361
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.308
Gnomad SAS
AF:
0.220
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.449
Gnomad OTH
AF:
0.442
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.432
AC:
65689
AN:
151968
Hom.:
14593
Cov.:
32
AF XY:
0.418
AC XY:
31016
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.490
Gnomad4 AMR
AF:
0.361
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.307
Gnomad4 SAS
AF:
0.222
Gnomad4 FIN
AF:
0.311
Gnomad4 NFE
AF:
0.449
Gnomad4 OTH
AF:
0.441
Alfa
AF:
0.436
Hom.:
1798
Bravo
AF:
0.444
Asia WGS
AF:
0.291
AC:
1011
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
5.9
DANN
Benign
0.37

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: rs914051; hg19: chr9-17062834; API