rs72624894

Variant names:

• chr3-64836792-C-T
• rs72624894
• ENST00000481312.2:n.563+26941C>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.563+26941C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,186 control chromosomes in the GnomAD database, including 1,069 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 0.081 (1069 hom., cov: 33)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.807+26941C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000481312.2	n.563+26941C>T		intron_variant	Intron 3 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.573+26941C>T		intron_variant	Intron 3 of 4	2
ADAMTS9-AS2	ENST00000650103.1	n.742+26941C>T		intron_variant	Intron 3 of 11

Frequencies

GnomAD3 genomes AF: 0.0811 AC: 12327 AN: 152068 Hom.: 1061 Cov.: 33

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0540

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0811 AC: 12344 AN: 152186 Hom.: 1069 Cov.: 33 AF XY: 0.0886 AC XY: 6593 AN XY: 74390

African (AFR) AF: 0.0293 AC: 1218 AN: 41546

American (AMR) AF: 0.207 AC: 3160 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2228 AN: 5170

South Asian (SAS) AF: 0.112 AC: 540 AN: 4814

European-Finnish (FIN) AF: 0.105 AC: 1116 AN: 10580

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0540 AC: 3673 AN: 68008

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.0690 Hom.: 80

Bravo AF: 0.0860

Asia WGS AF: 0.288 AC: 997 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs72624894; hg19: chr3-64822467;