Variant chr18-1977712-G-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 0.066 in 147,004 control chromosomes in the GnomAD database, including 673 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 0.066 ( 673 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

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 (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.1977712G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000263745	ENST00000584867.1 linkuse as main transcript	n.197-71066C>A	intron_variant	2
ENSG00000266602	ENST00000653330.1 linkuse as main transcript	n.453-71275G>T	intron_variant
ENSG00000266602	ENST00000657750.1 linkuse as main transcript	n.561-71275G>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0660

AC:

9693

AN:

146894

Hom.:

669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0187

Gnomad AMR

AF:

0.0277

Gnomad ASJ

AF:

0.0106

Gnomad EAS

AF:

0.00738

Gnomad SAS

AF:

0.0114

Gnomad FIN

AF:

0.0324

Gnomad MID

AF:

0.0892

Gnomad NFE

AF:

0.0241

Gnomad OTH

AF:

0.0481

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

GnomAD4 genome

AF:

0.0660

AC:

9703

AN:

147004

Hom.:

673

Cov.:

AF XY:

0.0642

AC XY:

4599

AN XY:

71644

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.0276

Gnomad4 ASJ

AF:

0.0106

Gnomad4 EAS

AF:

0.00740

Gnomad4 SAS

AF:

0.0112

Gnomad4 FIN

AF:

0.0324

Gnomad4 NFE

AF:

0.0241

Gnomad4 OTH

AF:

0.0475

Alfa

AF:

0.0131

Hom.:

Bravo

AF:

0.0685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.59

DANN

Benign

0.56

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