3-64699265-C-T

Position:

• chr3-64699265-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038264.1(ADAMTS9-AS2):​n.469+13927C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,942 control chromosomes in the GnomAD database, including 13,903 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 0.42 (13903 hom., cov: 33)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+13927C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.404+13927C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63892 AN: 151824 Hom.: 13883 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.421 AC: 63947 AN: 151942 Hom.: 13903 Cov.: 33 AF XY: 0.416 AC XY: 30928 AN XY: 74262

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.444

Alfa AF: 0.455 Hom.: 8769

Bravo AF: 0.426

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4688504; hg19: chr3-64684941;