3-64719689-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.138

Genes affected

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

ACMG classification

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	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+34351C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88514 AN: 151860 Hom.: 28370 Cov.: 32

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.: 32 AF XY: 0.588 AC XY: 43680 AN XY: 74256

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

Submissions by phenotype

not provided Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	11
Dann	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6795735; hg19: chr3-64705365;