Variant 1-65691047-C-T 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 0.419 in 151,752 control chromosomes in the GnomAD database, including 14,016 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 0.42 ( 14016 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

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).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.65691047C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63444

AN:

151632

Hom.:

14000

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.462

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.867

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.382

Gnomad OTH

AF:

0.405

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

GnomAD4 genome

AF:

0.419

AC:

63512

AN:

151752

Hom.:

14016

Cov.:

AF XY:

0.428

AC XY:

31711

AN XY:

74142

show subpopulations

Gnomad4 AFR

AF:

0.390

Gnomad4 AMR

AF:

0.462

Gnomad4 ASJ

AF:

0.375

Gnomad4 EAS

AF:

0.867

Gnomad4 SAS

AF:

0.461

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.382

Gnomad4 OTH

AF:

0.410

Alfa

AF:

0.366

Hom.:

5420

Bravo

AF:

0.414

Asia WGS

AF:

0.546

AC:

1643

AN:

3018

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.51

DANN

Benign

0.50

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