Variant chr14-74303274-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000557177.1(VRTN):c.-164+98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 208,518 control chromosomes in the GnomAD database, including 10,900 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7255 hom., cov: 33)

Exomes 𝑓: 0.35 ( 3645 hom. )

Consequence

VRTN
ENST00000557177.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.586

Variant links:

Genes affected

VRTN (HGNC:20223): (vertebrae development associated) Predicted to enable sequence-specific DNA binding activity and transposase activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in chromatin. [provided by Alliance of Genome Resources, Apr 2022]

VRTN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 14-74303274-G-A is Benign according to our data. Variant chr14-74303274-G-A is described in ClinVar as [Benign]. Clinvar id is 1234864.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VRTN	XM_011536911.3 linkuse as main transcript	c.-164+124G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VRTN	ENST00000557177.1 linkuse as main transcript	c.-164+98G>A		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

45087

AN:

152082

Hom.:

7263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.354

GnomAD4 exome

AF:

0.350

AC:

19689

AN:

56318

Hom.:

3645

AF XY:

0.349

AC XY:

9855

AN XY:

28244

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.271

Gnomad4 ASJ exome

AF:

0.428

Gnomad4 EAS exome

AF:

0.230

Gnomad4 SAS exome

AF:

0.363

Gnomad4 FIN exome

AF:

0.304

Gnomad4 NFE exome

AF:

0.375

Gnomad4 OTH exome

AF:

0.357

GnomAD4 genome

AF:

0.296

AC:

45079

AN:

152200

Hom.:

7255

Cov.:

AF XY:

0.294

AC XY:

21868

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.425

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.362

Gnomad4 OTH

AF:

0.354

Alfa

AF:

0.298

Hom.:

1038

Bravo

AF:

0.288

Asia WGS

AF:

0.307

AC:

1065

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.9

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over