15-88838476-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001369268.1(ACAN):c.71-187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,256 control chromosomes in the GnomAD database, including 213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.040 (213 hom., cov: 32)
• Consequence: ACAN NM_001369268.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0580

Genes affected

ACAN (HGNC:319): (aggrecan) This gene is a member of the aggrecan/versican proteoglycan family. The encoded protein is an integral part of the extracellular matrix in cartilagenous tissue and it withstands compression in cartilage. Mutations in this gene may be involved in skeletal dysplasia and spinal degeneration. Multiple alternatively spliced transcript variants that encode different protein isoforms have been observed in this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 15-88838476-G-A is Benign according to our data. Variant chr15-88838476-G-A is described in ClinVar as [Benign]. Clinvar id is 1261820.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACAN	NM_001369268.1	c.71-187G>A		intron_variant		ENST00000560601.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACAN	ENST00000560601.4	c.71-187G>A		intron_variant		3	NM_001369268.1	P1

Frequencies

GnomAD3 genomes AF: 0.0396 AC: 6021 AN: 152138 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0396 AC: 6026 AN: 152256 Hom.: 213 Cov.: 32 AF XY: 0.0404 AC XY: 3010 AN XY: 74446

Gnomad4 AFR AF: 0.0886

Gnomad4 AMR AF: 0.0315

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.0896

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.00635 Hom.: 2

Bravo AF: 0.0424

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.65

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: rs115252131; hg19: chr15-89381707;