3-64922932-G-A

Position:

• chr3-64922932-G-A

Variant summary

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

The NR_038264.1(ADAMTS9-AS2):​n.897+55675G>A 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 152,114 control chromosomes in the GnomAD database, including 4,627 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 (4627 hom., cov: 32)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

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

LOC105377124 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.897+55675G>A		intron_variant, non_coding_transcript_variant
LOC105377124	XR_007095948.1	n.262+19572C>T		intron_variant, non_coding_transcript_variant
LOC105377124	XR_001740437.2	n.262+19572C>T		intron_variant, non_coding_transcript_variant
LOC105377124	XR_007095946.1	n.262+19572C>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.832+55675G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36206 AN: 151994 Hom.: 4619 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.238 AC: 36246 AN: 152114 Hom.: 4627 Cov.: 32 AF XY: 0.243 AC XY: 18083 AN XY: 74356

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.261

Alfa AF: 0.229 Hom.: 495

Bravo AF: 0.244

Asia WGS AF: 0.337 AC: 1171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2218266; hg19: chr3-64908607;