3-64699265-C-T

Variant names:

• chr3-64699265-C-T
• rs4688504
• ENST00000460833.2:n.460+13927C>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+13927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,942 control chromosomes in the GnomAD database, including 13,903 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 0.42 (13903 hom., cov: 33)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 2 publications found

Genes affected

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

ENSG00000300305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+13927C>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+13927C>T		intron_variant	Intron 1 of 1	1
ADAMTS9-AS2	ENST00000481312.2	n.225+13927C>T		intron_variant	Intron 1 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.235+13927C>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63892 AN: 151824 Hom.: 13883 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.421 AC: 63947 AN: 151942 Hom.: 13903 Cov.: 33 AF XY: 0.416 AC XY: 30928 AN XY: 74262

African (AFR) AF: 0.322 AC: 13353 AN: 41420

American (AMR) AF: 0.483 AC: 7386 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2327 AN: 5158

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4052 AN: 10536

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32308 AN: 67944

Other (OTH) AF: 0.444 AC: 939 AN: 2116

Alfa AF: 0.455 Hom.: 8769

Bravo AF: 0.426

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.58
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4688504; hg19: chr3-64684941;