3-64695029-C-T

Variant names:

• chr3-64695029-C-T
• rs4521216
• ENST00000460833.2:n.460+9691C>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+9691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,258 control chromosomes in the GnomAD database, including 19,476 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 0.50 (19476 hom., cov: 29)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+9691C>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+9691C>T		intron_variant	Intron 1 of 1	1
ADAMTS9-AS2	ENST00000481312.2	n.225+9691C>T		intron_variant	Intron 1 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.235+9691C>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75134 AN: 151144 Hom.: 19456 Cov.: 29

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.497 AC: 75200 AN: 151258 Hom.: 19476 Cov.: 29 AF XY: 0.507 AC XY: 37470 AN XY: 73876

African (AFR) AF: 0.442 AC: 18234 AN: 41274

American (AMR) AF: 0.551 AC: 8381 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1917 AN: 3464

East Asian (EAS) AF: 0.897 AC: 4604 AN: 5134

South Asian (SAS) AF: 0.753 AC: 3596 AN: 4778

European-Finnish (FIN) AF: 0.493 AC: 5095 AN: 10326

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31773 AN: 67778

Other (OTH) AF: 0.527 AC: 1099 AN: 2086

Alfa AF: 0.477 Hom.: 10535

Bravo AF: 0.497

Asia WGS AF: 0.797 AC: 2768 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.6
DANN	Benign	0.67
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4521216; hg19: chr3-64680705;