rs1011689

chr10-96000719-G-C

Variant summary

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

The NM_001349008.3(CC2D2B):c.2850-3433G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,946 control chromosomes in the GnomAD database, including 28,037 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 0.61 (28037 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CC2D2B NM_001349008.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

CC2D2B (HGNC:31666): (coiled-coil and C2 domain containing 2B) Predicted to be involved in non-motile cilium assembly and protein localization to ciliary transition zone. Predicted to be active in ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

ENTPD1-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CC2D2B	NM_001349008.3	c.2850-3433G>C		intron_variant		ENST00000646931.3
ENTPD1-AS1	NR_038444.1	n.296+88547C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CC2D2B	ENST00000646931.3	c.2850-3433G>C		intron_variant			NM_001349008.3	P1
ENTPD1-AS1	ENST00000669711.1	n.300+88547C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91933 AN: 151826 Hom.: 27987 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.612

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.606 AC: 92039 AN: 151944 Hom.: 28037 Cov.: 31 AF XY: 0.605 AC XY: 44951 AN XY: 74262

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.615

Alfa AF: 0.600 Hom.: 3379

Bravo AF: 0.609

Asia WGS AF: 0.670 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	13
Dann	Benign	0.76

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: rs1011689; hg19: chr10-97760476;