Variant chr3-64719689-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 NR_038264.1(ADAMTS9-AS2):n.469+34351C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,978 control chromosomes in the GnomAD database, including 28,430 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.58 ( 28430 hom., cov: 32)

Consequence

ADAMTS9-AS2
NR_038264.1 intron, non_coding_transcript

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -0.138

Variant links:

Genes affected

ADAMTS9-AS2 (HGNC:42435): (ADAMTS9 antisense RNA 2)

ADAMTS9-AS2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1 linkuse as main transcript	n.469+34351C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1 linkuse as main transcript	n.404+34351C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88514

AN:

151860

Hom.:

28370

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.550

Gnomad AMR

AF:

0.675

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.756

Gnomad SAS

AF:

0.746

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.723

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.606

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

GnomAD4 genome

AF:

0.583

AC:

88633

AN:

151978

Hom.:

28430

Cov.:

AF XY:

0.588

AC XY:

43680

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.819

Gnomad4 AMR

AF:

0.676

Gnomad4 ASJ

AF:

0.654

Gnomad4 EAS

AF:

0.756

Gnomad4 SAS

AF:

0.747

Gnomad4 FIN

AF:

0.373

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.607

Alfa

AF:

0.475

Hom.:

28295

Bravo

AF:

0.618

Asia WGS

AF:

0.777

AC:

2697

AN:

3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

DANN

Benign

0.54

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over