3-112623094-A-C

Position:

• chr3-112623094-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199511.3(CCDC80):​c.2036-3990T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,916 control chromosomes in the GnomAD database, including 15,828 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 0.43 (15828 hom., cov: 30)
• Consequence: CCDC80 NM_199511.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC80	NM_199511.3	c.2036-3990T>G		intron_variant		ENST00000206423.8	NP_955805.1
CCDC80	NM_199512.3	c.2036-3990T>G		intron_variant			NP_955806.1
CCDC80	XM_047447495.1	c.2069-3990T>G		intron_variant			XP_047303451.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC80	ENST00000206423.8	c.2036-3990T>G		intron_variant		1	NM_199511.3	ENSP00000206423	P1
CCDC80	ENST00000439685.6	c.2036-3990T>G		intron_variant		1		ENSP00000411814	P1
CCDC80	ENST00000461431.1	c.228-3990T>G		intron_variant		3		ENSP00000420123

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65815 AN: 151796 Hom.: 15802 Cov.: 30

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.434 AC: 65868 AN: 151916 Hom.: 15828 Cov.: 30 AF XY: 0.436 AC XY: 32350 AN XY: 74240

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.401

Alfa AF: 0.500 Hom.: 38645

Bravo AF: 0.408

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.51

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: rs9870432; hg19: chr3-112341941;