Variant 12-69133998-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 0.377 in 151,882 control chromosomes in the GnomAD database, including 11,660 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 0.38 ( 11660 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.69133998C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57222

AN:

151764

Hom.:

11663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.481

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.415

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

GnomAD4 genome

AF:

0.377

AC:

57235

AN:

151882

Hom.:

11660

Cov.:

AF XY:

0.387

AC XY:

28691

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.412

Gnomad4 EAS

AF:

0.710

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.439

Gnomad4 NFE

AF:

0.390

Gnomad4 OTH

AF:

0.409

Alfa

AF:

0.396

Hom.:

16963

Bravo

AF:

0.374

Asia WGS

AF:

0.560

AC:

1948

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.7

DANN

Benign

0.54

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