rs2039617

Variant names:

• chr10-95999446-G-A
• rs2039617
• NM_001349008.3:c.2849+3194G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-95999446-G-A
• chr10-95999446-G-C
• chr10-95999446-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349008.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CC2D2B	NM_001349008.3	MANE Select	c.2849+3194G>A		intron	N/A	NP_001335937.1	Q6DHV5-5
	ENTPD1-AS1	NR_038444.1		n.296+89820C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CC2D2B	ENST00000646931.3	MANE Select	c.2849+3194G>A		intron	N/A	ENSP00000496666.2	Q6DHV5-5
	CC2D2B	ENST00000636965.1	TSL:5	c.2049-4706G>A		intron	N/A	ENSP00000490447.1	A0A5S8K7B6
	ENTPD1-AS1	ENST00000416301.5	TSL:2	n.275+89820C>T		intron	N/A

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

African (AFR) AF: 0.363 AC: 14922 AN: 41130

American (AMR) AF: 0.169 AC: 2565 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 532 AN: 3446

East Asian (EAS) AF: 0.798 AC: 4125 AN: 5166

South Asian (SAS) AF: 0.265 AC: 1260 AN: 4752

European-Finnish (FIN) AF: 0.179 AC: 1806 AN: 10092

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5439 AN: 67534

Other (OTH) AF: 0.202 AC: 421 AN: 2086

Alfa AF: 0.108 Hom.: 1511

Bravo AF: 0.213

Asia WGS AF: 0.532 AC: 1839 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.78
DANN	Benign	0.14
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2039617; hg19: chr10-97759203;