rs10501618

Variant names:

• chr11-86405701-T-C
• rs10501618
• NM_001156474.2:c.882-1913T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

CCDC81 (HGNC:26281): (coiled-coil domain containing 81) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000309946 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC81	NM_001156474.2	c.882-1913T>C		intron_variant	Intron 7 of 14	ENST00000445632.7	NP_001149946.1
CCDC81	NM_021827.5	c.612-1913T>C		intron_variant	Intron 6 of 13		NP_068599.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC81	ENST00000445632.7	c.882-1913T>C		intron_variant	Intron 7 of 14	1	NM_001156474.2	ENSP00000415528.2

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

African (AFR) AF: 0.264 AC: 10929 AN: 41438

American (AMR) AF: 0.413 AC: 6296 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5170

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2811 AN: 10510

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26492 AN: 67956

Other (OTH) AF: 0.389 AC: 820 AN: 2110

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
PhyloP100		-0.23
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: rs10501618; hg19: chr11-86116743;