chr3-64744216-G-A

Position:

• chr3-64744216-G-A

Variant summary

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

The NR_038264.1(ADAMTS9-AS2):​n.470-55249G>A 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 0.679 in 152,070 control chromosomes in the GnomAD database, including 35,650 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 0.68 (35650 hom., cov: 34)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS9-AS2	NR_038264.1	n.470-55249G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.405-55249G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103216 AN: 151952 Hom.: 35618 Cov.: 34

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.679 AC: 103296 AN: 152070 Hom.: 35650 Cov.: 34 AF XY: 0.676 AC XY: 50238 AN XY: 74318

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.661

Alfa AF: 0.714 Hom.: 28747

Bravo AF: 0.672

Asia WGS AF: 0.602 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7638389; hg19: chr3-64729892;