rs7118648

Positions:

• chr11-96375264-T-C
• chr11-96375264-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC82	NM_024725.4	c.992-1797A>G		intron_variant		ENST00000646818.2	NP_079001.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC82	ENST00000646818.2	c.992-1797A>G		intron_variant			NM_024725.4	ENSP00000496393

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

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.00810

Gnomad4 SAS AF: 0.0732

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.0770

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.0685 Hom.: 422

Bravo AF: 0.0762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.51

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: rs7118648; hg19: chr11-96108428;