3-64728139-T-C

Variant names:

• chr3-64728139-T-C
• rs7372321
• ENST00000460833.2:n.460+42801T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000770932.1(ENSG00000300325):​n.794A>G variant causes a non coding transcript exon 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: ENSG00000300325 ENST00000770932.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

Genes affected

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

ENSG00000300325 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770932.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	NR_038264.1		n.469+42801T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000460833.2	TSL:1	n.460+42801T>C		intron	N/A
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.225+42801T>C		intron	N/A
	ENSG00000300325	ENST00000770932.1		n.794A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.535 AC: 28077 AN: 52494 Hom.: 2925 Cov.: 0

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

African (AFR) AF: 0.537 AC: 7998 AN: 14886

American (AMR) AF: 0.566 AC: 3844 AN: 6788

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 1340 AN: 2200

East Asian (EAS) AF: 0.547 AC: 1182 AN: 2162

South Asian (SAS) AF: 0.522 AC: 1357 AN: 2598

European-Finnish (FIN) AF: 0.495 AC: 1412 AN: 2850

Middle Eastern (MID) AF: 0.599 AC: 103 AN: 172

European-Non Finnish (NFE) AF: 0.518 AC: 10187 AN: 19658

Other (OTH) AF: 0.556 AC: 477 AN: 858

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7372321; hg19: chr3-64713815;