Variant rs2732550 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000702237.1(ENSG00000289526):n.133A>C 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 0.678 in 151,494 control chromosomes in the GnomAD database, including 36,132 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 0.68 ( 36132 hom., cov: 28)

Consequence

ENST00000702237.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.162

Variant links:

Genes affected

(HGNC:):

links:

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC105376626	XR_001748180.2 linkuse as main transcript	n.421A>C	non_coding_transcript_exon_variant	1/4
LOC105376626	XR_007062653.1 linkuse as main transcript	n.421A>C	non_coding_transcript_exon_variant	1/5
LOC105376626	XR_007062654.1 linkuse as main transcript	n.421A>C	non_coding_transcript_exon_variant	1/5

Ensembl

Transcript	HGVSc	Effect	#exon/exons
ENST00000702237.1 linkuse as main transcript	n.133A>C	non_coding_transcript_exon_variant	1/3
ENST00000685560.1 linkuse as main transcript	n.153A>C	non_coding_transcript_exon_variant	1/3
ENST00000687081.1 linkuse as main transcript	n.422A>C	non_coding_transcript_exon_variant	1/2
ENST00000701115.1 linkuse as main transcript	n.133A>C	non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

102539

AN:

151376

Hom.:

36085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.872

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.672

Gnomad ASJ

AF:

0.643

Gnomad EAS

AF:

0.791

Gnomad SAS

AF:

0.783

Gnomad FIN

AF:

0.545

Gnomad MID

AF:

0.736

Gnomad NFE

AF:

0.568

Gnomad OTH

AF:

0.685

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.678

AC:

102639

AN:

151494

Hom.:

36132

Cov.:

AF XY:

0.680

AC XY:

50328

AN XY:

74022

show subpopulations

Gnomad4 AFR

AF:

0.872

Gnomad4 AMR

AF:

0.672

Gnomad4 ASJ

AF:

0.643

Gnomad4 EAS

AF:

0.790

Gnomad4 SAS

AF:

0.781

Gnomad4 FIN

AF:

0.545

Gnomad4 NFE

AF:

0.568

Gnomad4 OTH

AF:

0.688

Alfa

AF:

0.627

Hom.:

3841

Bravo

AF:

0.693

Asia WGS

AF:

0.776

AC:

2696

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.2

DANN

Benign

0.74

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over