rs10501618

chr11-86405701-T-C

Variant summary

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

The NM_001156474.2(CCDC81):c.882-1913T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,942 control chromosomes in the GnomAD database, including 9,514 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 0.35 (9514 hom., cov: 32)
• Consequence: CCDC81 NM_001156474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

CCDC81 (HGNC:26281): (coiled-coil domain containing 81) Located in centrosome. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC81	NM_001156474.2	c.882-1913T>C		intron_variant		ENST00000445632.7
CCDC81	NM_021827.5	c.612-1913T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC81	ENST00000445632.7	c.882-1913T>C		intron_variant		1	NM_001156474.2	P1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52532 AN: 151824 Hom.: 9509 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.346 AC: 52560 AN: 151942 Hom.: 9514 Cov.: 32 AF XY: 0.344 AC XY: 25506 AN XY: 74250

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.389

Alfa AF: 0.370 Hom.: 2134

Bravo AF: 0.351

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.79
Dann	Benign	0.65

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: rs10501618; hg19: chr11-86116743;