Variant rs4743348 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000652827.1(ENSG00000237461):n.378-14127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,056 control chromosomes in the GnomAD database, including 8,748 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 0.33 ( 8748 hom., cov: 32)

Consequence

ENSG00000237461
ENST00000652827.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130

Variant links:

Genes affected

ENSG00000237461 (HGNC:):

ENSG00000237461 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=-0.71).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987011	XR_001746548.2 link	n.616-14127G>A		intron_variant
LOC107987011	XR_007061697.1 link	n.2150-14127G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000237461	ENST00000652827.1 link	n.378-14127G>A		intron_variant
STX17-DT	ENST00000655615.1 link	n.310-14127G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.334

AC:

50732

AN:

151938

Hom.:

8744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.383

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

GnomAD4 genome

AF:

0.334

AC:

50759

AN:

152056

Hom.:

8748

Cov.:

AF XY:

0.329

AC XY:

24488

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.331

Gnomad4 AMR

AF:

0.383

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.281

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.337

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.331

Hom.:

1032

Bravo

AF:

0.350

Asia WGS

AF:

0.270

AC:

938

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.76

DANN

Benign

0.58

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