chr11-96375264-T-C

Variant names:

• chr11-96375264-T-C
• rs7118648
• NM_024725.4:c.992-1797A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024725.4(CCDC82):​c.992-1797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,250 control chromosomes in the GnomAD database, including 456 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 0.074 (456 hom., cov: 32)
• Consequence: CCDC82 NM_024725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 10 publications found

Genes affected

CCDC82 (HGNC:26282): (coiled-coil domain containing 82) Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0892 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024725.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC82	NM_024725.4	MANE Select	c.992-1797A>G		intron	N/A	NP_079001.2
	CCDC82	NM_001318736.2		c.992-1797A>G		intron	N/A	NP_001305665.1
	CCDC82	NM_001437542.1		c.992-1797A>G		intron	N/A	NP_001424471.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC82	ENST00000646818.2	MANE Select	c.992-1797A>G		intron	N/A	ENSP00000496393.1
	CCDC82	ENST00000423339.2	TSL:1	c.992-1797A>G		intron	N/A	ENSP00000397156.2
	CCDC82	ENST00000278520.9	TSL:5	c.992-1797A>G		intron	N/A	ENSP00000278520.5

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11199 AN: 152132 Hom.: 456 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00827

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0736 AC: 11200 AN: 152250 Hom.: 456 Cov.: 32 AF XY: 0.0709 AC XY: 5277 AN XY: 74468

African (AFR) AF: 0.0917 AC: 3809 AN: 41550

American (AMR) AF: 0.0576 AC: 882 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3468

East Asian (EAS) AF: 0.00810 AC: 42 AN: 5188

South Asian (SAS) AF: 0.0732 AC: 353 AN: 4822

European-Finnish (FIN) AF: 0.0286 AC: 304 AN: 10620

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5237 AN: 67986

Other (OTH) AF: 0.0692 AC: 146 AN: 2110

Alfa AF: 0.0702 Hom.: 620

Bravo AF: 0.0762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		-0.31
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: rs7118648; hg19: chr11-96108428;