rs9783117

Variant names:

• chr1-169399063-T-C
• rs9783117
• NM_001300969.2:c.1216-1672A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300969.2. 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
	CCDC181	NM_001300969.2	MANE Select	c.1216-1672A>G		intron	N/A	NP_001287898.1	Q5TID7-1
	CCDC181	NM_001394007.1		c.1216-1672A>G		intron	N/A	NP_001380936.1	Q5TID7-1
	CCDC181	NM_001300968.1		c.1216-1675A>G		intron	N/A	NP_001287897.1	B2R917

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC181	ENST00000367806.8	TSL:1 MANE Select	c.1216-1672A>G		intron	N/A	ENSP00000356780.3	Q5TID7-1
	CCDC181	ENST00000367805.7	TSL:1	c.1216-1675A>G		intron	N/A	ENSP00000356779.3	Q5TID7-3
	CCDC181	ENST00000545005.5	TSL:1	c.1216-1675A>G		intron	N/A	ENSP00000442297.1	Q5TID7-3

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

African (AFR) AF: 0.173 AC: 7189 AN: 41498

American (AMR) AF: 0.146 AC: 2233 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4056 AN: 5172

South Asian (SAS) AF: 0.229 AC: 1107 AN: 4830

European-Finnish (FIN) AF: 0.0911 AC: 965 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0611 AC: 4154 AN: 67998

Other (OTH) AF: 0.140 AC: 296 AN: 2114

Alfa AF: 0.0914 Hom.: 3696

Bravo AF: 0.143

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.1
DANN	Benign	0.82
PhyloP100		-0.46
Mutation Taster		=100/0	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: rs9783117; hg19: chr1-169368301;