4-21977694-G-T

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.445+28235G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,004 control chromosomes in the GnomAD database, including 25,277 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 0.54 ( 25277 hom., cov: 32)

Consequence

ENSG00000250039
ENST00000510705.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.106
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=-0.78).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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
ENSG00000250039ENST00000510705.3 linkn.445+28235G>T intron_variant Intron 1 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.540
AC:
81983
AN:
151884
Hom.:
25274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.208
Gnomad AMI
AF:
0.610
Gnomad AMR
AF:
0.645
Gnomad ASJ
AF:
0.694
Gnomad EAS
AF:
0.692
Gnomad SAS
AF:
0.590
Gnomad FIN
AF:
0.697
Gnomad MID
AF:
0.585
Gnomad NFE
AF:
0.669
Gnomad OTH
AF:
0.570
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.539
AC:
81997
AN:
152004
Hom.:
25277
Cov.:
32
AF XY:
0.546
AC XY:
40532
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.208
Gnomad4 AMR
AF:
0.644
Gnomad4 ASJ
AF:
0.694
Gnomad4 EAS
AF:
0.693
Gnomad4 SAS
AF:
0.590
Gnomad4 FIN
AF:
0.697
Gnomad4 NFE
AF:
0.669
Gnomad4 OTH
AF:
0.568
Alfa
AF:
0.641
Hom.:
41331
Bravo
AF:
0.525

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
11
DANN
Benign
0.71

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: rs4696998; hg19: chr4-21979317; API