rs4132228

Variant names:

• chr3-64722438-C-T
• rs4132228
• ENST00000460833.2:n.460+37100C>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+37100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,880 control chromosomes in the GnomAD database, including 16,478 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 0.44 (16478 hom., cov: 31)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 21 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+37100C>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+37100C>T		intron_variant	Intron 1 of 1	1
ADAMTS9-AS2	ENST00000481312.2	n.225+37100C>T		intron_variant	Intron 1 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.235+37100C>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66243 AN: 151762 Hom.: 16439 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.437 AC: 66339 AN: 151880 Hom.: 16478 Cov.: 31 AF XY: 0.441 AC XY: 32750 AN XY: 74220

African (AFR) AF: 0.637 AC: 26399 AN: 41430

American (AMR) AF: 0.480 AC: 7305 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3036 AN: 5130

South Asian (SAS) AF: 0.671 AC: 3228 AN: 4814

European-Finnish (FIN) AF: 0.245 AC: 2588 AN: 10554

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20332 AN: 67950

Other (OTH) AF: 0.462 AC: 973 AN: 2108

Alfa AF: 0.361 Hom.: 36939

Bravo AF: 0.461

Asia WGS AF: 0.659 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.60
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4132228; hg19: chr3-64708114;