3-64932947-G-C

Position:

• chr3-64932947-G-C

Variant summary

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

The ENST00000481312.2(ADAMTS9-AS2):​n.653+65690G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,790 control chromosomes in the GnomAD database, including 31,372 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 0.64 (31372 hom., cov: 30)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

ADAMTS9-AS2 (HGNC:):

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 = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.897+65690G>C		intron_variant
LOC105377124	XR_001740437.2	n.262+9557C>G		intron_variant
LOC105377124	XR_007095946.1	n.262+9557C>G		intron_variant
LOC105377124	XR_007095948.1	n.262+9557C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000481312.2	n.653+65690G>C		intron_variant		1
ADAMTS9-AS2	ENST00000474768.5	n.664-40865G>C		intron_variant		2
ADAMTS9-AS2	ENST00000650103.1	n.832+65690G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96468 AN: 151672 Hom.: 31355 Cov.: 30

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.636 AC: 96533 AN: 151790 Hom.: 31372 Cov.: 30 AF XY: 0.630 AC XY: 46714 AN XY: 74154

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.651

Alfa AF: 0.589 Hom.: 1722

Bravo AF: 0.635

Asia WGS AF: 0.582 AC: 2025 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	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs812651; hg19: chr3-64918622;