13-43877684-C-T

Variant names:

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

Variant summary

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

The NM_144974.5(CCDC122):​c.-200+1947G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,586 control chromosomes in the GnomAD database, including 19,763 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 0.51 (19763 hom., cov: 33)
  • Failed GnomAD Quality Control
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC122	NM_144974.5	c.-200+1947G>A		intron_variant	Intron 1 of 6	ENST00000444614.8	NP_659411.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC122	ENST00000444614.8	c.-200+1947G>A		intron_variant	Intron 1 of 6	5	NM_144974.5	ENSP00000407763.2
CCDC122	ENST00000476570.2	n.61+1947G>A		intron_variant	Intron 1 of 6	5
CCDC122	ENST00000611737.1	n.97+1947G>A		intron_variant	Intron 1 of 1	3
ENSG00000274001	ENST00000613918.1	n.*31G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76542 AN: 151466 Hom.: 19723 Cov.: 33

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.522

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.506 AC: 76632 AN: 151586 Hom.: 19763 Cov.: 33 AF XY: 0.509 AC XY: 37726 AN XY: 74098

African (AFR) AF: 0.595 AC: 24522 AN: 41244

American (AMR) AF: 0.566 AC: 8625 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2142 AN: 3466

East Asian (EAS) AF: 0.591 AC: 3042 AN: 5148

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4822

European-Finnish (FIN) AF: 0.411 AC: 4307 AN: 10490

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29788 AN: 67858

Other (OTH) AF: 0.526 AC: 1107 AN: 2106

Alfa AF: 0.452 Hom.: 5450

Bravo AF: 0.520

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.013
DANN	Benign	0.34
PhyloP100		-2.1
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: rs4942254; hg19: chr13-44451820;