rs7113656

Variant names:

• chr11-85883696-T-C
• rs7113656
• NM_001286159.2:c.343+1021T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC83	NM_001286159.2	c.343+1021T>C		intron_variant	Intron 4 of 10	ENST00000342404.8	NP_001273088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC83	ENST00000342404.8	c.343+1021T>C		intron_variant	Intron 4 of 10	1	NM_001286159.2	ENSP00000344512.3
CCDC83	ENST00000526729.1	c.226+1021T>C		intron_variant	Intron 2 of 7	1		ENSP00000434373.1
CCDC83	ENST00000280245.8	c.343+1021T>C		intron_variant	Intron 4 of 11	2		ENSP00000280245.4
CCDC83	ENST00000529676.2	n.86+10401T>C		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.487 AC: 20209 AN: 41464

American (AMR) AF: 0.274 AC: 4190 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3468

East Asian (EAS) AF: 0.110 AC: 567 AN: 5178

South Asian (SAS) AF: 0.176 AC: 848 AN: 4814

European-Finnish (FIN) AF: 0.470 AC: 4965 AN: 10554

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19131 AN: 67950

Other (OTH) AF: 0.311 AC: 656 AN: 2108

Alfa AF: 0.294 Hom.: 4164

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
PhyloP100		-1.0
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: rs7113656; hg19: chr11-85594739;