rs10861032

Variant summary

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

The ENST00000650784.1(ENSG00000286197):​n.698A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,080 control chromosomes in the GnomAD database, including 5,607 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 0.24 ( 5607 hom., cov: 32)

Consequence


ENST00000650784.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.972
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 = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
C12orf42XM_011538294.3 linkuse as main transcriptc.36+5384A>G intron_variant XP_011536596.1
C12orf42XM_011538306.2 linkuse as main transcriptc.36+5384A>G intron_variant XP_011536608.1
C12orf42XM_011538312.3 linkuse as main transcriptc.36+5384A>G intron_variant XP_011536614.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000650784.1 linkuse as main transcriptn.698A>G non_coding_transcript_exon_variant 4/4

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36502
AN:
151962
Hom.:
5587
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.392
Gnomad AMI
AF:
0.130
Gnomad AMR
AF:
0.195
Gnomad ASJ
AF:
0.217
Gnomad EAS
AF:
0.516
Gnomad SAS
AF:
0.443
Gnomad FIN
AF:
0.120
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.145
Gnomad OTH
AF:
0.232
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.240
AC:
36568
AN:
152080
Hom.:
5607
Cov.:
32
AF XY:
0.244
AC XY:
18177
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.392
Gnomad4 AMR
AF:
0.195
Gnomad4 ASJ
AF:
0.217
Gnomad4 EAS
AF:
0.515
Gnomad4 SAS
AF:
0.441
Gnomad4 FIN
AF:
0.120
Gnomad4 NFE
AF:
0.145
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.178
Hom.:
3397
Bravo
AF:
0.250
Asia WGS
AF:
0.501
AC:
1742
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
0.51
DANN
Benign
0.64

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: rs10861032; hg19: chr12-103912506; API