NM_001394954.1:c.2882+122G>T

Variant names:

• chr4-76332310-C-A
• rs10518146
• NM_001394954.1:c.2882+122G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394954.1(CCDC158):​c.2882+122G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000018 in 556,238 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000018 (0 hom.)
• Consequence: CCDC158 NM_001394954.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 0 publications found

Genes affected

CCDC158 (HGNC:26374): (coiled-coil domain containing 158)

CCDC158 Gene-Disease associations (from GenCC):

• renal tubule disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394954.1. 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
	CCDC158	NM_001394954.1	MANE Select	c.2882+122G>T		intron	N/A	NP_001381883.1	A0A804HIY6
	CCDC158	NM_001042784.1		c.2870+122G>T		intron	N/A	NP_001036249.1	Q5M9N0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC158	ENST00000682701.1	MANE Select	c.2882+122G>T		intron	N/A	ENSP00000507278.1	A0A804HIY6
	CCDC158	ENST00000504667.2	TSL:1	n.2748+122G>T		intron	N/A
	CCDC158	ENST00000388914.7	TSL:5	c.2870+122G>T		intron	N/A	ENSP00000373566.2	Q5M9N0-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000180 AC: 1 AN: 556238 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 299804

African (AFR) AF: 0.00 AC: 0 AN: 11854

American (AMR) AF: 0.00 AC: 0 AN: 17016

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17202

East Asian (EAS) AF: 0.0000357 AC: 1 AN: 28020

South Asian (SAS) AF: 0.00 AC: 0 AN: 51168

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45668

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3548

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 353046

Other (OTH) AF: 0.00 AC: 0 AN: 28716

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		0.10

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: rs10518146; hg19: chr4-77253463;