Variant chr6-155954557-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000663591.1(ENSG00000287092):n.399-42291C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 419,724 control chromosomes in the GnomAD database, including 35,078 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 0.41 ( 13144 hom., cov: 32)

Exomes 𝑓: 0.40 ( 21934 hom. )

Consequence

ENSG00000287092
ENST00000663591.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.00

Variant links:

Genes affected

ENSG00000287092 (HGNC:):

ENSG00000287092 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.23).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928923	XR_001744423.2 linkuse as main transcript	n.406-121663C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287092	ENST00000663591.1 linkuse as main transcript	n.399-42291C>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62518

AN:

151862

Hom.:

13123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.429

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.363

Gnomad EAS

AF:

0.597

Gnomad SAS

AF:

0.395

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.420

GnomAD3 exomes

AF:

0.405

AC:

44913

AN:

110970

Hom.:

9559

AF XY:

0.399

AC XY:

24408

AN XY:

61168

show subpopulations

Gnomad AFR exome

AF:

0.353

Gnomad AMR exome

AF:

0.482

Gnomad ASJ exome

AF:

0.327

Gnomad EAS exome

AF:

0.569

Gnomad SAS exome

AF:

0.369

Gnomad FIN exome

AF:

0.383

Gnomad NFE exome

AF:

0.383

Gnomad OTH exome

AF:

0.393

GnomAD4 exome

AF:

0.398

AC:

106560

AN:

267740

Hom.:

21934

Cov.:

AF XY:

0.397

AC XY:

61344

AN XY:

154712

show subpopulations

Gnomad4 AFR exome

AF:

0.353

Gnomad4 AMR exome

AF:

0.489

Gnomad4 ASJ exome

AF:

0.331

Gnomad4 EAS exome

AF:

0.587

Gnomad4 SAS exome

AF:

0.379

Gnomad4 FIN exome

AF:

0.401

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.412

AC:

62587

AN:

151984

Hom.:

13144

Cov.:

AF XY:

0.413

AC XY:

30712

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.378

Gnomad4 AMR

AF:

0.475

Gnomad4 ASJ

AF:

0.363

Gnomad4 EAS

AF:

0.598

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.422

Alfa

AF:

0.404

Hom.:

2998

Bravo

AF:

0.422

Asia WGS

AF:

0.462

AC:

1606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.69

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