rs6807798

chr3-112641079-G-T

Variant summary

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

The NM_199511.3(CCDC80):c.-764C>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.231 in 152,198 control chromosomes in the GnomAD database, including 4,603 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 0.23 (4602 hom., cov: 32)
  • Exomes 𝑓: 0.26 (1 hom.)
• Consequence: CCDC80 NM_199511.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.89

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=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC80	NM_199511.3	c.-764C>A		5_prime_UTR_variant	1/8	ENST00000206423.8
CCDC80	NM_199512.3	c.-167C>A		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC80	ENST00000206423.8	c.-764C>A		5_prime_UTR_variant	1/8	1	NM_199511.3	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35069 AN: 152038 Hom.: 4601 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.262 AC: 11 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.219 AC XY: 7 AN XY: 32

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.308

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.231 AC: 35074 AN: 152156 Hom.: 4602 Cov.: 32 AF XY: 0.229 AC XY: 17058 AN XY: 74380

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.313

Alfa AF: 0.294 Hom.: 9026

Bravo AF: 0.230

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	20
Dann	Benign	0.93

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: rs6807798; hg19: chr3-112359926;