rs2242592

Variant summary

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

The ENST00000546284.1(ENSG00000256757):​n.244+2741G>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 0.571 in 151,916 control chromosomes in the GnomAD database, including 26,799 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 0.57 ( 26799 hom., cov: 31)

Consequence


ENST00000546284.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358
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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000546284.1 linkuse as main transcriptn.244+2741G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.571
AC:
86699
AN:
151798
Hom.:
26799
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.323
Gnomad AMI
AF:
0.710
Gnomad AMR
AF:
0.608
Gnomad ASJ
AF:
0.654
Gnomad EAS
AF:
0.458
Gnomad SAS
AF:
0.600
Gnomad FIN
AF:
0.658
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.699
Gnomad OTH
AF:
0.619
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.571
AC:
86717
AN:
151916
Hom.:
26799
Cov.:
31
AF XY:
0.569
AC XY:
42270
AN XY:
74234
show subpopulations
Gnomad4 AFR
AF:
0.322
Gnomad4 AMR
AF:
0.608
Gnomad4 ASJ
AF:
0.654
Gnomad4 EAS
AF:
0.457
Gnomad4 SAS
AF:
0.602
Gnomad4 FIN
AF:
0.658
Gnomad4 NFE
AF:
0.699
Gnomad4 OTH
AF:
0.616
Alfa
AF:
0.682
Hom.:
47168
Bravo
AF:
0.560
Asia WGS
AF:
0.508
AC:
1766
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.36
DANN
Benign
0.32

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: rs2242592; hg19: chr11-113279430; API