rs4411878

Positions:

• chr3-64717989-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+32651C>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 0.238 in 152,082 control chromosomes in the GnomAD database, including 4,653 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 0.24 (4653 hom., cov: 32)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+32651C>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+32651C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36129 AN: 151962 Hom.: 4649 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.238 AC: 36140 AN: 152082 Hom.: 4653 Cov.: 32 AF XY: 0.238 AC XY: 17662 AN XY: 74348

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.267

Alfa AF: 0.258 Hom.: 11298

Bravo AF: 0.231

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.32
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4411878; hg19: chr3-64703665;