5-91759840-C-T

Variant summary

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

The ENST00000651690.1(ENSG00000286121):​n.459-24017C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,972 control chromosomes in the GnomAD database, including 3,743 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 0.20 ( 3743 hom., cov: 32)

Consequence


ENST00000651690.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.336
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=-0.99).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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
ENST00000651690.1 linkuse as main transcriptn.459-24017C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.204
AC:
31053
AN:
151854
Hom.:
3742
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0795
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.275
Gnomad ASJ
AF:
0.237
Gnomad EAS
AF:
0.279
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.287
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.245
Gnomad OTH
AF:
0.225
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.204
AC:
31048
AN:
151972
Hom.:
3743
Cov.:
32
AF XY:
0.208
AC XY:
15438
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.0793
Gnomad4 AMR
AF:
0.275
Gnomad4 ASJ
AF:
0.237
Gnomad4 EAS
AF:
0.278
Gnomad4 SAS
AF:
0.211
Gnomad4 FIN
AF:
0.287
Gnomad4 NFE
AF:
0.245
Gnomad4 OTH
AF:
0.226
Alfa
AF:
0.239
Hom.:
5733
Bravo
AF:
0.199
Asia WGS
AF:
0.248
AC:
858
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.6
DANN
Benign
0.57

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: rs6881283; hg19: chr5-91055657; API