rs2279531

Variant names:

• chr3-112637923-T-A
• rs2279531
• NM_199511.3:c.1878+105A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-112637923-T-A
• chr3-112637923-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 9 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: 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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC80	NM_199511.3	c.1878+105A>T		intron_variant	Intron 2 of 7	ENST00000206423.8	NP_955805.1
CCDC80	NM_199512.3	c.1878+105A>T		intron_variant	Intron 2 of 7		NP_955806.1
CCDC80	XM_047447495.1	c.1911+105A>T		intron_variant	Intron 1 of 6		XP_047303451.1

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1351386 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 664036

African (AFR) AF: 0.00 AC: 0 AN: 30032

American (AMR) AF: 0.00 AC: 0 AN: 27290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19768

East Asian (EAS) AF: 0.00 AC: 0 AN: 38992

South Asian (SAS) AF: 0.00 AC: 0 AN: 67404

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40932

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4998

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1065868

Other (OTH) AF: 0.00 AC: 0 AN: 56102

GnomAD4 genome Cov.: 32

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
DANN	Benign	0.88
PhyloP100		-0.014
PromoterAI		-0.0082	Neutral

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: rs2279531; hg19: chr3-112356770;