13-43859494-C-A

Position:

• chr13-43859494-C-A

Variant summary

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

The NM_144974.5(CCDC122):​c.555+178G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,684 control chromosomes in the GnomAD database, including 1,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).

• Frequency: Genomes: 𝑓 0.15 (1935 hom., cov: 33)
• Consequence: CCDC122 NM_144974.5 intron
• Clinical Significance: Uncertain risk allele no assertion criteria provided O:1
• Conservation: PhyloP100: -0.322

Genes affected

CCDC122 (HGNC:26478): (coiled-coil domain containing 122) This gene encodes a protein that contains a coiled-coil domain. Naturally occurring mutations in this gene are associated with leprosy. [provided by RefSeq, Apr 2017]

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 (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC122	NM_144974.5	c.555+178G>T		intron_variant		ENST00000444614.8	NP_659411.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC122	ENST00000444614.8	c.555+178G>T		intron_variant		5	NM_144974.5	ENSP00000407763	P1
CCDC122	ENST00000470137.5	n.484+178G>T		intron_variant, non_coding_transcript_variant		5
CCDC122	ENST00000476570.2	n.815+178G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23181 AN: 151564 Hom.: 1933 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.153 AC: 23208 AN: 151684 Hom.: 1935 Cov.: 33 AF XY: 0.159 AC XY: 11790 AN XY: 74094

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.153

Alfa AF: 0.145 Hom.: 3436

Bravo AF: 0.150

Asia WGS AF: 0.240 AC: 833 AN: 3472

ClinVar

Significance: Uncertain risk allele

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Leprosy, susceptibility to, 1 Other:1

Uncertain risk allele, no assertion criteria provided

case-control

Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta

Jun 10, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.42

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: rs3088362; hg19: chr13-44433630;