Variant chr8-127042277-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.441 in 151,686 control chromosomes in the GnomAD database, including 15,607 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 0.44 ( 15607 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.127042277A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
PCAT1	ENST00000643594.2 linkuse as main transcript	n.216-21771A>G	intron_variant
PCAT1	ENST00000644627.1 linkuse as main transcript	n.712-21771A>G	intron_variant
PCAT1	ENST00000644733.1 linkuse as main transcript	n.126-21771A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66788

AN:

151568

Hom.:

15576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.596

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.434

Gnomad ASJ

AF:

0.353

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.490

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.459

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

GnomAD4 genome

AF:

0.441

AC:

66876

AN:

151686

Hom.:

15607

Cov.:

AF XY:

0.434

AC XY:

32217

AN XY:

74148

show subpopulations

Gnomad4 AFR

AF:

0.596

Gnomad4 AMR

AF:

0.434

Gnomad4 ASJ

AF:

0.353

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.391

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.396

Gnomad4 OTH

AF:

0.461

Alfa

AF:

0.406

Hom.:

26254

Bravo

AF:

0.458

Asia WGS

AF:

0.363

AC:

1261

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.4

DANN

Benign

0.62

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