Variant 3-195076-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 0.639 in 152,040 control chromosomes in the GnomAD database, including 32,676 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 0.64 ( 32676 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.195076C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHL1-AS2	ENST00000663345.1 linkuse as main transcript	n.115+1531G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

97172

AN:

151924

Hom.:

32656

Cov.:

show subpopulations

Gnomad AFR

AF:

0.427

Gnomad AMI

AF:

0.648

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.708

Gnomad EAS

AF:

0.963

Gnomad SAS

AF:

0.730

Gnomad FIN

AF:

0.758

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.635

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

GnomAD4 genome

AF:

0.639

AC:

97228

AN:

152040

Hom.:

32676

Cov.:

AF XY:

0.648

AC XY:

48155

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.427

Gnomad4 AMR

AF:

0.701

Gnomad4 ASJ

AF:

0.708

Gnomad4 EAS

AF:

0.964

Gnomad4 SAS

AF:

0.729

Gnomad4 FIN

AF:

0.758

Gnomad4 NFE

AF:

0.702

Gnomad4 OTH

AF:

0.638

Alfa

AF:

0.683

Hom.:

47929

Bravo

AF:

0.627

Asia WGS

AF:

0.831

AC:

2885

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

DANN

Benign

0.18

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