rs281366

Variant summary

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

The ENST00000602353.1(ENSG00000270091):​n.190G>A 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 0.04 in 152,198 control chromosomes in the GnomAD database, including 176 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 0.040 ( 176 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence


ENST00000602353.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.553
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=-0.78).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0823 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
ENST00000602353.1 linkuse as main transcriptn.190G>A non_coding_transcript_exon_variant 1/1
ENST00000602532.1 linkuse as main transcriptn.207G>A non_coding_transcript_exon_variant 1/25

Frequencies

GnomAD3 genomes
AF:
0.0400
AC:
6076
AN:
152080
Hom.:
176
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0847
Gnomad AMI
AF:
0.00439
Gnomad AMR
AF:
0.0240
Gnomad ASJ
AF:
0.00923
Gnomad EAS
AF:
0.0202
Gnomad SAS
AF:
0.0178
Gnomad FIN
AF:
0.0192
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0250
Gnomad OTH
AF:
0.0292
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
10
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
6
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0400
AC:
6082
AN:
152198
Hom.:
176
Cov.:
32
AF XY:
0.0377
AC XY:
2806
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.0846
Gnomad4 AMR
AF:
0.0241
Gnomad4 ASJ
AF:
0.00923
Gnomad4 EAS
AF:
0.0201
Gnomad4 SAS
AF:
0.0178
Gnomad4 FIN
AF:
0.0192
Gnomad4 NFE
AF:
0.0250
Gnomad4 OTH
AF:
0.0289
Alfa
AF:
0.0379
Hom.:
49
Bravo
AF:
0.0418
Asia WGS
AF:
0.0300
AC:
105
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
3.7
DANN
Benign
0.42

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: rs281366; hg19: chr17-19800394; API