3-64719689-C-T

Variant names:

• chr3-64719689-C-T
• rs6795735
• ENST00000460833.2:n.460+34351C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460833.2(ADAMTS9-AS2):​n.460+34351C>T variant causes a intron 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 ENST00000460833.2 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.138
• Publications: 167 publications found

Genes affected

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

ENSG00000300325 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+34351C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000460833.2	n.460+34351C>T		intron_variant	Intron 1 of 1	1
ADAMTS9-AS2	ENST00000481312.2	n.225+34351C>T		intron_variant	Intron 1 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.235+34351C>T		intron_variant	Intron 1 of 4	2

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

African (AFR) AF: 0.819 AC: 33961 AN: 41490

American (AMR) AF: 0.676 AC: 10302 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2269 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3883 AN: 5136

South Asian (SAS) AF: 0.747 AC: 3596 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3933 AN: 10554

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28691 AN: 67954

Other (OTH) AF: 0.607 AC: 1284 AN: 2116

Alfa AF: 0.487 Hom.: 69548

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

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Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.54
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6795735; hg19: chr3-64705365;