chr21-16868539-C-T

Variant summary

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

The ENST00000430064.1(ENSG00000232886):​n.50-1863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 152,278 control chromosomes in the GnomAD database, including 71,423 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 0.97 ( 71423 hom., cov: 33)

Consequence

ENSG00000232886
ENST00000430064.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000232886ENST00000430064.1 linkn.50-1863G>A intron_variant Intron 1 of 3 3

Frequencies

GnomAD3 genomes
AF:
0.967
AC:
147149
AN:
152158
Hom.:
71374
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.886
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.989
Gnomad ASJ
AF:
0.997
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.987
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.974
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.967
AC:
147255
AN:
152278
Hom.:
71423
Cov.:
33
AF XY:
0.968
AC XY:
72044
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.886
Gnomad4 AMR
AF:
0.989
Gnomad4 ASJ
AF:
0.997
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
1.00
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
1.00
Gnomad4 OTH
AF:
0.974
Alfa
AF:
0.968
Hom.:
10136
Bravo
AF:
0.962
Asia WGS
AF:
0.993
AC:
3453
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.18
DANN
Benign
0.65

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: rs451387; hg19: chr21-18240859; API