13-43877684-C-A

Variant names:

• chr13-43877684-C-A
• rs4942254
• NM_144974.5:c.-200+1947G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144974.5(CCDC122):​c.-200+1947G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CCDC122 NM_144974.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 11 publications found

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]

ENSG00000274001 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144974.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC122	NM_144974.5	MANE Select	c.-200+1947G>T		intron	N/A	NP_659411.2	Q5T0U0-1
	CCDC122	NM_001350617.2		c.-294+1734G>T		intron	N/A	NP_001337546.1
	CCDC122	NM_001350618.2		c.-294+1604G>T		intron	N/A	NP_001337547.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC122	ENST00000444614.8	TSL:5 MANE Select	c.-200+1947G>T		intron	N/A	ENSP00000407763.2	Q5T0U0-1
	CCDC122	ENST00000928435.1		c.-200+1734G>T		intron	N/A	ENSP00000598494.1
	CCDC122	ENST00000962405.1		c.-200+1604G>T		intron	N/A	ENSP00000632464.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.012
DANN	Benign	0.46
PhyloP100		-2.1

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: rs4942254; hg19: chr13-44451820;