rs2218497

Positions:

• chr13-43854657-G-A
• chr13-43854657-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144974.5(CCDC122):​c.672+4124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,810 control chromosomes in the GnomAD database, including 10,973 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 0.38 (10973 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCDC122 NM_144974.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC122	NM_144974.5	c.672+4124C>T		intron_variant		ENST00000444614.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC122	ENST00000444614.8	c.672+4124C>T		intron_variant		5	NM_144974.5	P1
CCDC122	ENST00000476570.2	n.2898C>T		non_coding_transcript_exon_variant	7/7	5
CCDC122	ENST00000470137.5	n.601+4124C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 56995 AN: 151692 Hom.: 10957 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.374

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.376 AC: 57046 AN: 151810 Hom.: 10973 Cov.: 31 AF XY: 0.385 AC XY: 28536 AN XY: 74162

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.380

Alfa AF: 0.229 Hom.: 487

Bravo AF: 0.377

Asia WGS AF: 0.510 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs2218497; hg19: chr13-44428793;