3-65032728-A-G

Variant names:

• chr3-65032728-A-G
• rs1517931
• XR_007095950.1:n.368T>C

Variant summary

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

The XR_007095950.1(LOC124909390):​n.368T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,044 control chromosomes in the GnomAD database, including 10,234 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 0.36 (10234 hom., cov: 32)
• Consequence: LOC124909390 XR_007095950.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 1 publications found

Genes affected

LOC124909390 (HGNC:):

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650103.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000650103.1		n.1947+13077A>G		intron	N/A
	ADAMTS9-AS2	ENST00000770413.1		n.1613+13077A>G		intron	N/A
	ADAMTS9-AS2	ENST00000770449.1		n.1028-123A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54585 AN: 151926 Hom.: 10215 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.359 AC: 54642 AN: 152044 Hom.: 10234 Cov.: 32 AF XY: 0.359 AC XY: 26696 AN XY: 74306

African (AFR) AF: 0.444 AC: 18433 AN: 41480

American (AMR) AF: 0.282 AC: 4311 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3462

East Asian (EAS) AF: 0.295 AC: 1524 AN: 5170

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4822

European-Finnish (FIN) AF: 0.436 AC: 4611 AN: 10576

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22323 AN: 67946

Other (OTH) AF: 0.362 AC: 765 AN: 2112

Alfa AF: 0.331 Hom.: 26747

Bravo AF: 0.354

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.85
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1517931; hg19: chr3-65018403;