rs11234454

chr11-85868261-C-Achr11-85868261-C-T

Variant summary

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

The NM_001286159.2(CCDC83):c.95+3043C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,056 control chromosomes in the GnomAD database, including 25,430 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 0.57 (25430 hom., cov: 33)
• Consequence: CCDC83 NM_001286159.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC83	NM_001286159.2	c.95+3043C>A		intron_variant		ENST00000342404.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC83	ENST00000342404.8	c.95+3043C>A		intron_variant		1	NM_001286159.2	P1
CCDC83	ENST00000280245.8	c.95+3043C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87295 AN: 151938 Hom.: 25393 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.575 AC: 87389 AN: 152056 Hom.: 25430 Cov.: 33 AF XY: 0.580 AC XY: 43093 AN XY: 74344

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.569

Alfa AF: 0.549 Hom.: 50341

Bravo AF: 0.567

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.84
Dann	Benign	0.34

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: rs11234454; hg19: chr11-85579304;