rs9533634

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC122	XM_047430113.1	c.*267A>G		3_prime_UTR_variant	Exon 7 of 7		XP_047286069.1
CCDC122	XM_047430112.1	c.*40+227A>G		intron_variant	Intron 7 of 7		XP_047286068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC122	ENST00000470137.5	n.*230A>G		downstream_gene_variant		5

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 v4.3

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;