rs2039617

chr10-95999446-G-Achr10-95999446-G-Cchr10-95999446-G-T

Variant summary

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

The NM_001349008.3(CC2D2B):c.2849+3194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 150,578 control chromosomes in the GnomAD database, including 5,304 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 0.21 (5304 hom., cov: 32)
• Consequence: CC2D2B NM_001349008.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871

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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CC2D2B	NM_001349008.3	c.2849+3194G>A		intron_variant		ENST00000646931.3
ENTPD1-AS1	NR_038444.1	n.296+89820C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CC2D2B	ENST00000646931.3	c.2849+3194G>A		intron_variant			NM_001349008.3	P1
ENTPD1-AS1	ENST00000669711.1	n.300+89820C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31081 AN: 150468 Hom.: 5279 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.207 AC: 31145 AN: 150578 Hom.: 5304 Cov.: 32 AF XY: 0.216 AC XY: 15849 AN XY: 73528

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.0805

Gnomad4 OTH AF: 0.202

Alfa AF: 0.105 Hom.: 1159

Bravo AF: 0.213

Asia WGS AF: 0.532 AC: 1839 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.78
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2039617; hg19: chr10-97759203;