Variant 8-40395182-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 0.323 in 152,046 control chromosomes in the GnomAD database, including 9,084 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 0.32 ( 9084 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0480

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 = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.40395182G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000253354	ENST00000518722.2 linkuse as main transcript	n.260-5833G>T	intron_variant	3
ENSG00000253354	ENST00000660702.1 linkuse as main transcript	n.282-5833G>T	intron_variant
ENSG00000289853	ENST00000701081.1 linkuse as main transcript	n.84+22527G>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49115

AN:

151926

Hom.:

9073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.704

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.304

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

GnomAD4 genome

AF:

0.323

AC:

49153

AN:

152046

Hom.:

9084

Cov.:

AF XY:

0.333

AC XY:

24764

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.427

Gnomad4 ASJ

AF:

0.289

Gnomad4 EAS

AF:

0.705

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.416

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.311

Alfa

AF:

0.340

Hom.:

11019

Bravo

AF:

0.319

Asia WGS

AF:

0.542

AC:

1880

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

DANN

Benign

0.51

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