3-64540934-G-A

Position:

• chr3-64540934-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_182920.2(ADAMTS9):​c.5521+161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,074 control chromosomes in the GnomAD database, including 35,796 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.64 (35796 hom., cov: 33)
• Consequence: ADAMTS9 NM_182920.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -4.04

Genes affected

ADAMTS9 (HGNC:13202): (ADAM metallopeptidase with thrombospondin type 1 motif 9) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. Members of the ADAMTS family have been implicated in the cleavage of proteoglycans, the control of organ shape during development, and the inhibition of angiogenesis. This gene is localized to chromosome 3p14.3-p14.2, an area known to be lost in hereditary renal tumors. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 3-64540934-G-A is Benign according to our data. Variant chr3-64540934-G-A is described in ClinVar as [Benign]. Clinvar id is 1228118.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9	NM_182920.2	c.5521+161C>T		intron_variant		ENST00000498707.5	NP_891550.1
ADAMTS9	NM_001318781.2	c.5437+161C>T		intron_variant			NP_001305710.1
ADAMTS9	XR_007095711.1	n.5780+161C>T		intron_variant, non_coding_transcript_variant
ADAMTS9	XR_245151.1	n.5864+161C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9	ENST00000498707.5	c.5521+161C>T		intron_variant		1	NM_182920.2	ENSP00000418735	P1
ADAMTS9	ENST00000295903.8	c.5437+161C>T		intron_variant		1		ENSP00000295903
ADAMTS9	ENST00000481060.2	c.2688+161C>T		intron_variant		2		ENSP00000417521

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97558 AN: 151956 Hom.: 35797 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.642 AC: 97561 AN: 152074 Hom.: 35796 Cov.: 33 AF XY: 0.634 AC XY: 47143 AN XY: 74336

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.665

Alfa AF: 0.661 Hom.: 2636

Bravo AF: 0.604

Asia WGS AF: 0.565 AC: 1967 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 08, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0010
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11130970; hg19: chr3-64526610; COSMIC: COSV55784123; COSMIC: COSV55784123;