Variant rs7260002 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000593746.1(ENSG00000268669):n.442A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.351 in 1,268,234 control chromosomes in the GnomAD database, including 83,254 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 0.46 ( 17776 hom., cov: 33)

Exomes 𝑓: 0.34 ( 65478 hom. )

Consequence

ENST00000593746.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.29

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 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
	ENST00000593746.1 linkuse as main transcript	n.442A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69410

AN:

151990

Hom.:

17750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.706

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.334

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.431

GnomAD4 exome

AF:

0.336

AC:

375376

AN:

1116126

Hom.:

65478

Cov.:

AF XY:

0.338

AC XY:

188872

AN XY:

559182

show subpopulations

Gnomad4 AFR exome

AF:

0.707

Gnomad4 AMR exome

AF:

0.294

Gnomad4 ASJ exome

AF:

0.279

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.336

Gnomad4 FIN exome

AF:

0.438

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.365

GnomAD4 genome

AF:

0.457

AC:

69489

AN:

152108

Hom.:

17776

Cov.:

AF XY:

0.454

AC XY:

33772

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.706

Gnomad4 AMR

AF:

0.358

Gnomad4 ASJ

AF:

0.277

Gnomad4 EAS

AF:

0.255

Gnomad4 SAS

AF:

0.335

Gnomad4 FIN

AF:

0.439

Gnomad4 NFE

AF:

0.364

Gnomad4 OTH

AF:

0.428

Alfa

AF:

0.435

Hom.:

1950

Bravo

AF:

0.459

Asia WGS

AF:

0.330

AC:

1145

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.67

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