Variant 6-14752642-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 0.873 in 152,084 control chromosomes in the GnomAD database, including 58,210 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 0.87 ( 58210 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.653

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.14752642C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000234261	ENST00000629853.2 linkuse as main transcript	n.313+37348G>A	intron_variant	5
ENSG00000234261	ENST00000689305.1 linkuse as main transcript	n.179-11591G>A	intron_variant
ENSG00000234261	ENST00000702363.1 linkuse as main transcript	n.187-21164G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.873

AC:

132677

AN:

151966

Hom.:

58179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.854

Gnomad AMR

AF:

0.870

Gnomad ASJ

AF:

0.940

Gnomad EAS

AF:

0.971

Gnomad SAS

AF:

0.913

Gnomad FIN

AF:

0.911

Gnomad MID

AF:

0.905

Gnomad NFE

AF:

0.906

Gnomad OTH

AF:

0.885

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

GnomAD4 genome

AF:

0.873

AC:

132756

AN:

152084

Hom.:

58210

Cov.:

AF XY:

0.875

AC XY:

65010

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.787

Gnomad4 AMR

AF:

0.870

Gnomad4 ASJ

AF:

0.940

Gnomad4 EAS

AF:

0.971

Gnomad4 SAS

AF:

0.913

Gnomad4 FIN

AF:

0.911

Gnomad4 NFE

AF:

0.906

Gnomad4 OTH

AF:

0.885

Alfa

AF:

0.896

Hom.:

26943

Bravo

AF:

0.863

Asia WGS

AF:

0.921

AC:

3202

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.6

DANN

Benign

0.32

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