1-169424650-C-T

Position:

• chr1-169424650-C-T

Variant summary

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

The NM_001300969.2(CCDC181):​c.117+161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 151,844 control chromosomes in the GnomAD database, including 1,550 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 0.074 (1550 hom., cov: 32)
• Consequence: CCDC181 NM_001300969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC181	NM_001300969.2	c.117+161G>A		intron_variant		ENST00000367806.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC181	ENST00000367806.8	c.117+161G>A		intron_variant		1	NM_001300969.2	A1

Frequencies

GnomAD3 genomes AF: 0.0740 AC: 11223 AN: 151726 Hom.: 1545 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0741 AC: 11248 AN: 151844 Hom.: 1550 Cov.: 32 AF XY: 0.0821 AC XY: 6096 AN XY: 74226

Gnomad4 AFR AF: 0.0788

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.0170

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.0320 Hom.: 105

Bravo AF: 0.0775

Asia WGS AF: 0.365 AC: 1262 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.68

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: rs16862153; hg19: chr1-169393888;