rs7113656

Positions:

• chr11-85883696-T-C

Variant summary

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

The NM_001286159.2(CCDC83):​c.343+1021T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,008 control chromosomes in the GnomAD database, including 9,830 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 0.34 (9830 hom., cov: 32)
• Consequence: CCDC83 NM_001286159.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

CCDC83 (HGNC:28535): (coiled-coil domain containing 83)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC83	NM_001286159.2	c.343+1021T>C		intron_variant		ENST00000342404.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC83	ENST00000342404.8	c.343+1021T>C		intron_variant		1	NM_001286159.2	P1
CCDC83	ENST00000526729.1	c.228+1021T>C		intron_variant		1
CCDC83	ENST00000280245.8	c.343+1021T>C		intron_variant		2
CCDC83	ENST00000529676.2	n.86+10401T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51872 AN: 151890 Hom.: 9803 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.342 AC: 51948 AN: 152008 Hom.: 9830 Cov.: 32 AF XY: 0.346 AC XY: 25707 AN XY: 74300

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.311

Alfa AF: 0.293 Hom.: 3768

Bravo AF: 0.337

Asia WGS AF: 0.181 AC: 627 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.69

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: rs7113656; hg19: chr11-85594739;