chr3-64849152-T-G

Position:

• chr3-64849152-T-G

Variant summary

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

The ENST00000481312.2(ADAMTS9-AS2):​n.564-18016T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,866 control chromosomes in the GnomAD database, including 18,762 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 0.49 (18762 hom., cov: 31)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

Genes affected

ADAMTS9-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.808-18016T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000481312.2	n.564-18016T>G		intron_variant		1
ADAMTS9-AS2	ENST00000474768.5	n.574-18016T>G		intron_variant		2
ADAMTS9-AS2	ENST00000650103.1	n.743-18016T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74706 AN: 151748 Hom.: 18730 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.493 AC: 74798 AN: 151866 Hom.: 18762 Cov.: 31 AF XY: 0.496 AC XY: 36837 AN XY: 74216

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.513

Alfa AF: 0.466 Hom.: 26424

Bravo AF: 0.501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs877523; hg19: chr3-64834827;