rs1208134

chr1-169459706-C-T

Variant summary

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

The ENST00000545005.5(CCDC181):c.-24+91G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.93 in 151,890 control chromosomes in the GnomAD database, including 65,740 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 0.93 (65737 hom., cov: 27)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: CCDC181 ENST00000545005.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC181	NM_001300968.1	c.-24+91G>A		intron_variant
CCDC181	XM_005245383.1	c.-24+91G>A		intron_variant
CCDC181	XM_017001938.2	c.-105+91G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC181	ENST00000545005.5	c.-24+91G>A		intron_variant		1		P4
CCDC181	ENST00000445428.5	n.268+91G>A		intron_variant, non_coding_transcript_variant		1
CCDC181	ENST00000437857.2	n.237+91G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141168 AN: 151766 Hom.: 65674 Cov.: 27

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.937

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 AF XY: 0.875 AC XY: 7 AN XY: 8

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.930 AC: 141290 AN: 151882 Hom.: 65737 Cov.: 27 AF XY: 0.930 AC XY: 69058 AN XY: 74224

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.937

Alfa AF: 0.934 Hom.: 88404

Bravo AF: 0.931

Asia WGS AF: 0.902 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.28
Dann	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1208134; hg19: chr1-169428944;