3-64728139-T-C

Position:

• chr3-64728139-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_038264.1(ADAMTS9-AS2):​n.469+42801T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.53 (2928 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+42801T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.404+42801T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 28077 AN: 52494 Hom.: 2925 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.556

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.535 AC: 28104 AN: 52542 Hom.: 2928 Cov.: 0 AF XY: 0.535 AC XY: 13853 AN XY: 25888

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.556

Alfa AF: 0.908 Hom.: 8672

Bravo AF: 0.902

Asia WGS AF: 0.440 AC: 766 AN: 1744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7372321; hg19: chr3-64713815;