XM_047430113.1:c.*267A>G

Variant names:

• chr13-43823679-T-C
• rs9533634
• XM_047430113.1:c.*267A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430113.1(CCDC122):​c.*267A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,190 control chromosomes in the GnomAD database, including 22,718 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 0.53 (22718 hom., cov: 34)
• Consequence: CCDC122 XM_047430113.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470137.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC122	ENST00000470137.5	TSL:5	n.*230A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80872 AN: 152072 Hom.: 22715 Cov.: 34

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.532 AC: 80901 AN: 152190 Hom.: 22718 Cov.: 34 AF XY: 0.523 AC XY: 38877 AN XY: 74390

African (AFR) AF: 0.404 AC: 16763 AN: 41524

American (AMR) AF: 0.443 AC: 6773 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5174

South Asian (SAS) AF: 0.530 AC: 2557 AN: 4826

European-Finnish (FIN) AF: 0.579 AC: 6132 AN: 10582

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43982 AN: 67998

Other (OTH) AF: 0.553 AC: 1170 AN: 2114

Alfa AF: 0.615 Hom.: 14214

Bravo AF: 0.518

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.38
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9533634; hg19: chr13-44397815; COSMIC: COSV72026052;