Variant 8-144476070-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The variant allele was found at a frequency of 0.488 in 314,232 control chromosomes in the GnomAD database, including 38,518 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 19244 hom., cov: 32)

Exomes 𝑓: 0.48 ( 19274 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.68

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 8-144476070-A-C is Benign according to our data. Variant chr8-144476070-A-C is described in ClinVar as [Benign]. Clinvar id is 362288.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.144476070A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.498

AC:

75490

AN:

151722

Hom.:

19218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.660

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.494

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.502

Gnomad OTH

AF:

0.482

GnomAD4 exome

AF:

0.480

AC:

77898

AN:

162394

Hom.:

19274

Cov.:

AF XY:

0.481

AC XY:

39277

AN XY:

81730

show subpopulations

Gnomad4 AFR exome

AF:

0.567

Gnomad4 AMR exome

AF:

0.379

Gnomad4 ASJ exome

AF:

0.479

Gnomad4 EAS exome

AF:

0.281

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.511

Gnomad4 NFE exome

AF:

0.503

Gnomad4 OTH exome

AF:

0.486

GnomAD4 genome

AF:

0.498

AC:

75565

AN:

151838

Hom.:

19244

Cov.:

AF XY:

0.493

AC XY:

36552

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.388

Gnomad4 ASJ

AF:

0.494

Gnomad4 EAS

AF:

0.289

Gnomad4 SAS

AF:

0.422

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.502

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.494

Hom.:

17832

Bravo

AF:

0.489

Asia WGS

AF:

0.405

AC:

1409

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Holoprosencephaly sequence

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.23

DANN

Benign

0.40

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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