3-64726228-C-T

Variant names:

• chr3-64726228-C-T
• rs4607103
• ENST00000460833.2:n.460+40890C>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+40890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,016 control chromosomes in the GnomAD database, including 6,723 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 0.29 (6723 hom., cov: 33)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 255 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460833.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	NR_038264.1		n.469+40890C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000460833.2	TSL:1	n.460+40890C>T		intron	N/A
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.225+40890C>T		intron	N/A
	ADAMTS9-AS2	ENST00000474768.5	TSL:2	n.235+40890C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43933 AN: 151898 Hom.: 6714 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.289 AC: 43965 AN: 152016 Hom.: 6723 Cov.: 33 AF XY: 0.294 AC XY: 21842 AN XY: 74290

African (AFR) AF: 0.299 AC: 12389 AN: 41446

American (AMR) AF: 0.318 AC: 4869 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3466

East Asian (EAS) AF: 0.364 AC: 1879 AN: 5156

South Asian (SAS) AF: 0.520 AC: 2502 AN: 4812

European-Finnish (FIN) AF: 0.264 AC: 2789 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16867 AN: 67980

Other (OTH) AF: 0.314 AC: 659 AN: 2102

Alfa AF: 0.270 Hom.: 21901

Bravo AF: 0.292

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.62
PhyloP100		-0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4607103;

hg19: chr3-64711904;