rs10014788

Variant summary

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

The ENST00000673514.1(ENSG00000288321):​n.1365-42234G>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 0.0834 in 151,926 control chromosomes in the GnomAD database, including 1,320 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 0.083 ( 1320 hom., cov: 32)

Consequence


ENST00000673514.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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
ENST00000673514.1 linkuse as main transcriptn.1365-42234G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0831
AC:
12616
AN:
151808
Hom.:
1308
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.247
Gnomad AMI
AF:
0.0165
Gnomad AMR
AF:
0.0338
Gnomad ASJ
AF:
0.00634
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0156
Gnomad FIN
AF:
0.0623
Gnomad MID
AF:
0.0318
Gnomad NFE
AF:
0.0149
Gnomad OTH
AF:
0.0613
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0834
AC:
12665
AN:
151926
Hom.:
1320
Cov.:
32
AF XY:
0.0831
AC XY:
6169
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.247
Gnomad4 AMR
AF:
0.0337
Gnomad4 ASJ
AF:
0.00634
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0156
Gnomad4 FIN
AF:
0.0623
Gnomad4 NFE
AF:
0.0149
Gnomad4 OTH
AF:
0.0607
Alfa
AF:
0.0176
Hom.:
25
Bravo
AF:
0.0876
Asia WGS
AF:
0.0260
AC:
92
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
0.84
DANN
Benign
0.43

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: rs10014788; hg19: chr4-33652745; API