rs12679744

Variant summary

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

The ENST00000668834.1(ENSG00000253983):​n.175+31452G>A 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 0.481 in 151,588 control chromosomes in the GnomAD database, including 17,736 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 0.48 ( 17736 hom., cov: 29)

Consequence


ENST00000668834.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.92
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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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
ENST00000668834.1 linkuse as main transcriptn.175+31452G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.481
AC:
72856
AN:
151470
Hom.:
17728
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.482
Gnomad AMI
AF:
0.556
Gnomad AMR
AF:
0.449
Gnomad ASJ
AF:
0.507
Gnomad EAS
AF:
0.615
Gnomad SAS
AF:
0.502
Gnomad FIN
AF:
0.408
Gnomad MID
AF:
0.617
Gnomad NFE
AF:
0.484
Gnomad OTH
AF:
0.493
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.481
AC:
72905
AN:
151588
Hom.:
17736
Cov.:
29
AF XY:
0.478
AC XY:
35380
AN XY:
74028
show subpopulations
Gnomad4 AFR
AF:
0.482
Gnomad4 AMR
AF:
0.449
Gnomad4 ASJ
AF:
0.507
Gnomad4 EAS
AF:
0.614
Gnomad4 SAS
AF:
0.501
Gnomad4 FIN
AF:
0.408
Gnomad4 NFE
AF:
0.484
Gnomad4 OTH
AF:
0.494
Alfa
AF:
0.478
Hom.:
10059
Bravo
AF:
0.486
Asia WGS
AF:
0.555
AC:
1930
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.78
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: rs12679744; hg19: chr8-75037406; API