3-64941350-C-T

Variant names:

• chr3-64941350-C-T
• rs704454
• ENST00000481312.2:n.654-67595C>T

Variant summary

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

The ENST00000481312.2(ADAMTS9-AS2):​n.654-67595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,098 control chromosomes in the GnomAD database, including 41,668 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 0.74 (41668 hom., cov: 33)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 8 publications found

Genes affected

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

ENSG00000300285 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.898-67595C>T		intron_variant	Intron 4 of 5
LOC105377124	XR_001740437.2	n.262+1154G>A		intron_variant	Intron 2 of 3
LOC105377124	XR_007095946.1	n.262+1154G>A		intron_variant	Intron 2 of 3
LOC105377124	XR_007095948.1	n.262+1154G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000481312.2	n.654-67595C>T		intron_variant	Intron 4 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.664-32462C>T		intron_variant	Intron 4 of 4	2
ADAMTS9-AS2	ENST00000650103.1	n.833-67595C>T		intron_variant	Intron 4 of 11

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112347 AN: 151980 Hom.: 41632 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.739 AC: 112438 AN: 152098 Hom.: 41668 Cov.: 33 AF XY: 0.737 AC XY: 54783 AN XY: 74346

African (AFR) AF: 0.755 AC: 31311 AN: 41498

American (AMR) AF: 0.801 AC: 12242 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2679 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3662 AN: 5152

South Asian (SAS) AF: 0.708 AC: 3411 AN: 4818

European-Finnish (FIN) AF: 0.675 AC: 7127 AN: 10564

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49417 AN: 68000

Other (OTH) AF: 0.746 AC: 1572 AN: 2106

Alfa AF: 0.737 Hom.: 83020

Bravo AF: 0.751

Asia WGS AF: 0.711 AC: 2472 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.77
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs704454; hg19: chr3-64927025;