NM_001017437.5:c.*1606A>G

Variant names:

• chr22-30378351-A-G
• rs9619104
• NM_001017437.5:c.*1606A>G

Variant summary

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

The NM_001017437.5(CCDC157):​c.*1606A>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 0.866 in 290,910 control chromosomes in the GnomAD database, including 109,845 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 0.88 (58719 hom., cov: 33)
  • Exomes 𝑓: 0.86 (51126 hom.)
• Consequence: CCDC157 NM_001017437.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

CCDC157 (HGNC:33854): (coiled-coil domain containing 157)

RNF215 (HGNC:33434): (ring finger protein 215) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in Golgi to vacuole transport; protein targeting to vacuole; and ubiquitin-dependent protein catabolic process. Predicted to be integral component of membrane. Predicted to be part of Golgi transport complex. Predicted to be active in endosome; membrane; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC157	NM_001017437.5	c.*1606A>G		3_prime_UTR_variant	Exon 12 of 12	ENST00000338306.8	NP_001017437.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC157	ENST00000338306.8	c.*1606A>G		3_prime_UTR_variant	Exon 12 of 12	5	NM_001017437.5	ENSP00000343087.3

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133201 AN: 152152 Hom.: 58661 Cov.: 33

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.879

GnomAD4 exome AF: 0.856 AC: 118717 AN: 138640 Hom.: 51126 Cov.: 0 AF XY: 0.865 AC XY: 66462 AN XY: 76858

Gnomad4 AFR exome AF: 0.976

Gnomad4 AMR exome AF: 0.858

Gnomad4 ASJ exome AF: 0.891

Gnomad4 EAS exome AF: 0.902

Gnomad4 SAS exome AF: 0.926

Gnomad4 FIN exome AF: 0.872

Gnomad4 NFE exome AF: 0.813

Gnomad4 OTH exome AF: 0.861

GnomAD4 genome AF: 0.876 AC: 133316 AN: 152270 Hom.: 58719 Cov.: 33 AF XY: 0.880 AC XY: 65544 AN XY: 74440

Gnomad4 AFR AF: 0.967

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.881

Alfa AF: 0.806 Hom.: 2852

Bravo AF: 0.876

Asia WGS AF: 0.923 AC: 3209 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	0.63
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9619104; hg19: chr22-30774340;