rs6807798

Variant names:

• chr3-112641079-G-T
• rs6807798
• NM_199511.3:c.-764C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199511.3(CCDC80):​c.-764C>A variant causes a 5 prime UTR premature start codon gain 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_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.89
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199511.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC80	NM_199511.3	MANE Select	c.-764C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	NP_955805.1	Q76M96-1
	CCDC80	NM_199511.3	MANE Select	c.-764C>A		5_prime_UTR	Exon 1 of 8	NP_955805.1	Q76M96-1
	CCDC80	NM_199512.3		c.-167C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	NP_955806.1	Q76M96-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC80	ENST00000206423.8	TSL:1 MANE Select	c.-764C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	ENSP00000206423.3	Q76M96-1
	CCDC80	ENST00000439685.6	TSL:1	c.-167C>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 8	ENSP00000411814.2	Q76M96-1
	CCDC80	ENST00000206423.8	TSL:1 MANE Select	c.-764C>A		5_prime_UTR	Exon 1 of 8	ENSP00000206423.3	Q76M96-1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 3 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.308 AC: 8 AN: 26

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.108 AC: 4485 AN: 41542

American (AMR) AF: 0.280 AC: 4285 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3468

East Asian (EAS) AF: 0.140 AC: 722 AN: 5170

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4824

European-Finnish (FIN) AF: 0.229 AC: 2414 AN: 10556

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20097 AN: 67990

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.289 Hom.: 11070

Bravo AF: 0.230

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	20
DANN	Benign	0.93
PhyloP100		6.9
PromoterAI		-0.21	Neutral
Mutation Taster		=293/7	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6807798; hg19: chr3-112359926;