rs9783117

Positions:

• chr1-169399063-T-C

Variant summary

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

The NM_001300969.2(CCDC181):​c.1216-1672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,182 control chromosomes in the GnomAD database, including 2,846 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 0.14 (2846 hom., cov: 32)
• Consequence: CCDC181 NM_001300969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

CCDC181 (HGNC:28051): (coiled-coil domain containing 181) Predicted to enable microtubule binding activity. Predicted to be located in manchette and sperm flagellum. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC181	NM_001300969.2	c.1216-1672A>G		intron_variant		ENST00000367806.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC181	ENST00000367806.8	c.1216-1672A>G		intron_variant		1	NM_001300969.2	A1
CCDC181	ENST00000367805.7	c.1216-1675A>G		intron_variant		1		P4
CCDC181	ENST00000545005.5	c.1216-1675A>G		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20572 AN: 152064 Hom.: 2840 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.135 AC: 20612 AN: 152182 Hom.: 2846 Cov.: 32 AF XY: 0.143 AC XY: 10615 AN XY: 74394

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0857 Hom.: 2385

Bravo AF: 0.143

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.1
DANN	Benign	0.82

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: rs9783117; hg19: chr1-169368301;