Variant chr5-63965502-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.576 in 151,620 control chromosomes in the GnomAD database, including 26,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.58 ( 26145 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.484

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 5-63965502-C-T is Benign according to our data. Variant chr5-63965502-C-T is described in ClinVar as [Benign]. Clinvar id is 1252728.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.63965502C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248285	ENST00000502882.1 linkuse as main transcript	n.97-7487G>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87204

AN:

151504

Hom.:

26104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.727

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.520

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.591

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.501

Gnomad OTH

AF:

0.571

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

GnomAD4 genome

AF:

0.576

AC:

87291

AN:

151620

Hom.:

26145

Cov.:

AF XY:

0.573

AC XY:

42469

AN XY:

74086

show subpopulations

Gnomad4 AFR

AF:

0.728

Gnomad4 AMR

AF:

0.520

Gnomad4 ASJ

AF:

0.535

Gnomad4 EAS

AF:

0.792

Gnomad4 SAS

AF:

0.589

Gnomad4 FIN

AF:

0.428

Gnomad4 NFE

AF:

0.501

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.517

Hom.:

21554

Bravo

AF:

0.589

Asia WGS

AF:

0.667

AC:

2318

AN:

3474

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

Mar 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

DANN

Benign

0.45

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