Variant chrY-13493019-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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 0.019 ( 0 hom., 638 hem., cov: 0)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.533

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=-0.89).

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0194 (638/32841) while in subpopulation AMR AF= 0.0442 (158/3578). AF 95% confidence interval is 0.0385. There are 0 homozygotes in gnomad4. There are 638 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 638 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.13493019C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0194

AC:

635

AN:

32780

Hom.:

Cov.:

AF XY:

0.0194

AC XY:

635

AN XY:

32780

show subpopulations

Gnomad AFR

AF:

0.00405

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.0442

Gnomad ASJ

AF:

0.00797

Gnomad EAS

AF:

0.000792

Gnomad SAS

AF:

0.0129

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.176

Gnomad NFE

AF:

0.0281

Gnomad OTH

AF:

0.0133

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

GnomAD4 genome

AF:

0.0194

AC:

638

AN:

32841

Hom.:

Cov.:

AF XY:

0.0194

AC XY:

638

AN XY:

32841

show subpopulations

Gnomad4 AFR

AF:

0.00403

Gnomad4 AMR

AF:

0.0442

Gnomad4 ASJ

AF:

0.00797

Gnomad4 EAS

AF:

0.000792

Gnomad4 SAS

AF:

0.0135

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0282

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.0359

Hom.:

1529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.9

DANN

Benign

0.56

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