chr3-64741410-A-T

Variant names:

• chr3-64741410-A-T
• rs7433808
• ENST00000460833.2:n.460+56072A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460833.2(ADAMTS9-AS2):​n.460+56072A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,078 control chromosomes in the GnomAD database, including 7,082 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 0.29 (7079 hom., cov: 32)
  • Exomes 𝑓: 0.28 (3 hom.)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+56072A>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000460833.2	n.460+56072A>T		intron_variant	Intron 1 of 1	1
ADAMTS9-AS2	ENST00000481312.2	n.225+56072A>T		intron_variant	Intron 1 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.235+56072A>T		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44222 AN: 151914 Hom.: 7070 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.283 AC: 13 AN: 46 Hom.: 3 AF XY: 0.333 AC XY: 12 AN XY: 36

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.206 AC: 7 AN: 34

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.291 AC: 44258 AN: 152032 Hom.: 7079 Cov.: 32 AF XY: 0.289 AC XY: 21475 AN XY: 74274

African (AFR) AF: 0.395 AC: 16378 AN: 41432

American (AMR) AF: 0.226 AC: 3458 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3470

East Asian (EAS) AF: 0.190 AC: 979 AN: 5160

South Asian (SAS) AF: 0.469 AC: 2251 AN: 4796

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10572

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16513 AN: 67996

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.257 Hom.: 699

Bravo AF: 0.293

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs7433808; hg19: chr3-64727086;