Variant chr6-68432116-T-G 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 0.386 in 151,658 control chromosomes in the GnomAD database, including 12,284 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 0.39 ( 12284 hom., cov: 30)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.447

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.68432116T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000288088	ENST00000654495.1 linkuse as main transcript	n.235+80673A>C	intron_variant
ENSG00000288088	ENST00000657302.1 linkuse as main transcript	n.112-90596A>C	intron_variant
ENSG00000288088	ENST00000669267.1 linkuse as main transcript	n.168+35051A>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58468

AN:

151540

Hom.:

12272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.853

Gnomad SAS

AF:

0.509

Gnomad FIN

AF:

0.369

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.376

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

GnomAD4 genome

AF:

0.386

AC:

58509

AN:

151658

Hom.:

12284

Cov.:

AF XY:

0.391

AC XY:

28953

AN XY:

74102

show subpopulations

Gnomad4 AFR

AF:

0.269

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.853

Gnomad4 SAS

AF:

0.510

Gnomad4 FIN

AF:

0.369

Gnomad4 NFE

AF:

0.394

Gnomad4 OTH

AF:

0.380

Alfa

AF:

0.392

Hom.:

22095

Bravo

AF:

0.394

Asia WGS

AF:

0.641

AC:

2224

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.0

DANN

Benign

0.57

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