Genetic Variant CCDC80:c.1878+105A>T (chr3-112637923-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_199511.3(CCDC80):c.1878+105A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CCDC80
NM_199511.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140

Publications

9 publications found

Variant links:

Genes affected

CCDC80 (HGNC:30649): (coiled-coil domain containing 80) Predicted to enable glycosaminoglycan binding activity. Predicted to act upstream of or within extracellular matrix organization; positive regulation of cell-substrate adhesion; and response to bacterium. Predicted to be located in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

CCDC80 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCDC80	NM_199511.3 link	c.1878+105A>T	intron_variant	Intron 2 of 7	ENST00000206423.8	NP_955805.1	Q76M96-1
CCDC80	NM_199512.3 link	c.1878+105A>T	intron_variant	Intron 2 of 7		NP_955806.1	Q76M96-1
CCDC80	XM_047447495.1 link	c.1911+105A>T	intron_variant	Intron 1 of 6		XP_047303451.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC80	ENST00000206423.8 link	c.1878+105A>T	intron_variant	Intron 2 of 7	1	NM_199511.3	ENSP00000206423.3	Q76M96-1
CCDC80	ENST00000439685.6 link	c.1878+105A>T	intron_variant	Intron 2 of 7	1		ENSP00000411814.2	Q76M96-1
CCDC80	ENST00000461431.1 link	c.69+105A>T	intron_variant	Intron 1 of 5	3		ENSP00000420123.1	H7C5K4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1351386

Hom.:

AF XY:

0.00

AC XY:

AN XY:

664036

African (AFR)

AF:

0.00

AC:

AN:

30032

American (AMR)

AF:

0.00

AC:

AN:

27290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19768

East Asian (EAS)

AF:

0.00

AC:

AN:

38992

South Asian (SAS)

AF:

0.00

AC:

AN:

67404

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40932

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4998

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1065868

Other (OTH)

AF:

0.00

AC:

AN:

56102

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

6.7

(source)

DANN

Benign

0.88

PhyloP100

-0.014

PromoterAI

-0.0082

Neutral

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over