Variant 10-97895891-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018058.7(CRTAC1):c.1311C>A(p.Gly437Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 1,611,826 control chromosomes in the GnomAD database, including 2,959 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 0.056 ( 270 hom., cov: 32)

Exomes 𝑓: 0.058 ( 2689 hom. )

Consequence

CRTAC1
NM_018058.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0640

Variant links:

Genes affected

CRTAC1 (HGNC:14882): (cartilage acidic protein 1) This gene encodes a glycosylated extracellular matrix protein that is found in the interterritorial matrix of articular deep zone cartilage. This protein is used as a marker to distinguish chondrocytes from osteoblasts and mesenchymal stem cells in culture. The presence of FG-GAP motifs and an RGD integrin-binding motif suggests that this protein may be involved in cell-cell or cell-matrix interactions. Copy number alterations in this gene have been observed in neurofibromatosis type 1-associated glomus tumors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

CRTAC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=-0.064 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.061 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRTAC1	NM_018058.7 linkuse as main transcript	c.1311C>A	p.Gly437Gly	synonymous_variant	10/15	ENST00000370597.8	NP_060528.3	Q9NQ79-1
CRTAC1	NM_001206528.3 linkuse as main transcript	c.1311C>A	p.Gly437Gly	synonymous_variant	10/15		NP_001193457.1	Q9NQ79-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CRTAC1	ENST00000370597.8 linkuse as main transcript	c.1311C>A	p.Gly437Gly	synonymous_variant	10/15	1	NM_018058.7	ENSP00000359629.3	Q9NQ79-1
CRTAC1	ENST00000309155.3 linkuse as main transcript	c.1287C>A	p.Gly429Gly	synonymous_variant	9/14	1		ENSP00000310810.3	A0A0C4DFP6
CRTAC1	ENST00000370591.6 linkuse as main transcript	c.1311C>A	p.Gly437Gly	synonymous_variant	10/15	5		ENSP00000359623.2	Q9NQ79-2
CRTAC1	ENST00000413387.5 linkuse as main transcript	c.999C>A	p.Gly333Gly	synonymous_variant	8/12	2		ENSP00000408445.1	Q5T4F6

Frequencies

GnomAD3 genomes

AF:

0.0558

AC:

8494

AN:

152124

Hom.:

272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0516

Gnomad AMI

AF:

0.0681

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0299

Gnomad FIN

AF:

0.0565

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0626

Gnomad OTH

AF:

0.0646

GnomAD3 exomes

AF:

0.0502

AC:

12592

AN:

250706

Hom.:

370

AF XY:

0.0509

AC XY:

6906

AN XY:

135630

show subpopulations

Gnomad AFR exome

AF:

0.0504

Gnomad AMR exome

AF:

0.0405

Gnomad ASJ exome

AF:

0.0478

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0308

Gnomad FIN exome

AF:

0.0632

Gnomad NFE exome

AF:

0.0640

Gnomad OTH exome

AF:

0.0561

GnomAD4 exome

AF:

0.0579

AC:

84451

AN:

1459584

Hom.:

2689

Cov.:

AF XY:

0.0576

AC XY:

41832

AN XY:

725822

show subpopulations

Gnomad4 AFR exome

AF:

0.0527

Gnomad4 AMR exome

AF:

0.0431

Gnomad4 ASJ exome

AF:

0.0502

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0317

Gnomad4 FIN exome

AF:

0.0597

Gnomad4 NFE exome

AF:

0.0628

Gnomad4 OTH exome

AF:

0.0541

GnomAD4 genome

AF:

0.0558

AC:

8488

AN:

152242

Hom.:

270

Cov.:

AF XY:

0.0553

AC XY:

4115

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0515

Gnomad4 AMR

AF:

0.0624

Gnomad4 ASJ

AF:

0.0476

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0295

Gnomad4 FIN

AF:

0.0565

Gnomad4 NFE

AF:

0.0626

Gnomad4 OTH

AF:

0.0644

Alfa

AF:

0.0599

Hom.:

410

Bravo

AF:

0.0560

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0680

EpiControl

AF:

0.0660

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

1.0

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over