18-60427176-A-G

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.114-52395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,704 control chromosomes in the GnomAD database, including 25,667 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 0.58 ( 25667 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.943
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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
ENSG00000285681ENST00000650201.1 linkn.114-52395A>G intron_variant Intron 1 of 3
ENSG00000285681ENST00000658928.1 linkn.157-52395A>G intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.580
AC:
87871
AN:
151586
Hom.:
25663
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.572
Gnomad AMI
AF:
0.458
Gnomad AMR
AF:
0.578
Gnomad ASJ
AF:
0.515
Gnomad EAS
AF:
0.759
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.525
Gnomad NFE
AF:
0.581
Gnomad OTH
AF:
0.562
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.579
AC:
87911
AN:
151704
Hom.:
25667
Cov.:
32
AF XY:
0.581
AC XY:
43043
AN XY:
74116
show subpopulations
Gnomad4 AFR
AF:
0.571
Gnomad4 AMR
AF:
0.578
Gnomad4 ASJ
AF:
0.515
Gnomad4 EAS
AF:
0.759
Gnomad4 SAS
AF:
0.485
Gnomad4 FIN
AF:
0.595
Gnomad4 NFE
AF:
0.581
Gnomad4 OTH
AF:
0.563
Alfa
AF:
0.581
Hom.:
3282
Bravo
AF:
0.576
Asia WGS
AF:
0.613
AC:
2131
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
4.2
DANN
Benign
0.63

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: rs1943232; hg19: chr18-58094409; API