rs17113027

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000693438.2(ENSG00000289301):​n.382A>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 0.0144 in 152,096 control chromosomes in the GnomAD database, including 45 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 0.014 ( 45 hom., cov: 31)

Consequence

ENSG00000289301
ENST00000693438.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449
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=-0.81).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (2190/152096) while in subpopulation AFR AF= 0.0489 (2025/41452). AF 95% confidence interval is 0.0471. There are 45 homozygotes in gnomad4. There are 1041 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.100373012T>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000289301ENST00000693438.2 linkuse as main transcriptn.382A>G non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.0144
AC:
2181
AN:
151978
Hom.:
44
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0488
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00721
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000623
Gnomad FIN
AF:
0.0000944
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.0129
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0144
AC:
2190
AN:
152096
Hom.:
45
Cov.:
31
AF XY:
0.0140
AC XY:
1041
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0489
Gnomad4 AMR
AF:
0.00720
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000623
Gnomad4 FIN
AF:
0.0000944
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.0118
Hom.:
4
Bravo
AF:
0.0165
Asia WGS
AF:
0.00289
AC:
10
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
1.8
DANN
Benign
0.66

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: rs17113027; hg19: chr10-102132769; API