13-43859494-C-A

Variant names:

• chr13-43859494-C-A
• rs3088362
• NM_144974.5:c.555+178G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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]

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

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.555+178G>T		intron	N/A	NP_659411.2	Q5T0U0-1
	CCDC122	NM_001350617.2		c.192+178G>T		intron	N/A	NP_001337546.1
	CCDC122	NM_001350618.2		c.192+178G>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.555+178G>T		intron	N/A	ENSP00000407763.2	Q5T0U0-1
	CCDC122	ENST00000928435.1		c.555+178G>T		intron	N/A	ENSP00000598494.1
	CCDC122	ENST00000962405.1		c.555+178G>T		intron	N/A	ENSP00000632464.1

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

African (AFR) AF: 0.123 AC: 5098 AN: 41420

American (AMR) AF: 0.210 AC: 3203 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1267 AN: 5164

South Asian (SAS) AF: 0.243 AC: 1163 AN: 4794

European-Finnish (FIN) AF: 0.164 AC: 1722 AN: 10506

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9626 AN: 67800

Other (OTH) AF: 0.153 AC: 322 AN: 2100

Alfa AF: 0.145 Hom.: 7107

Bravo AF: 0.150

Asia WGS AF: 0.240 AC: 833 AN: 3472

ClinVar

ClinVar submissions

Significance: Uncertain risk allele

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Leprosy, susceptibility to, 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.42
PhyloP100		-0.32
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: rs3088362; hg19: chr13-44433630;