rs5749078

Variant names:

• chr22-30365077-A-G
• rs5749078
• NM_001017437.5:c.-11-913A>G

Variant summary

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

The NM_001017437.5(CCDC157):​c.-11-913A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,208 control chromosomes in the GnomAD database, including 58,740 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 (58740 hom., cov: 31)
• Consequence: CCDC157 NM_001017437.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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.-11-913A>G		intron_variant	Intron 2 of 11	ENST00000338306.8	NP_001017437.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC157	ENST00000338306.8	c.-11-913A>G		intron_variant	Intron 2 of 11	5	NM_001017437.5	ENSP00000343087.3

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133199 AN: 152088 Hom.: 58681 Cov.: 31

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: 0.923

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.880

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.876 AC: 133316 AN: 152208 Hom.: 58740 Cov.: 31 AF XY: 0.881 AC XY: 65565 AN XY: 74430

African (AFR) AF: 0.967 AC: 40178 AN: 41542

American (AMR) AF: 0.872 AC: 13321 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3098 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4687 AN: 5180

South Asian (SAS) AF: 0.922 AC: 4450 AN: 4826

European-Finnish (FIN) AF: 0.888 AC: 9403 AN: 10592

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55360 AN: 67996

Other (OTH) AF: 0.881 AC: 1863 AN: 2114

Alfa AF: 0.851 Hom.: 7168

Bravo AF: 0.876

Asia WGS AF: 0.923 AC: 3211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0030
DANN	Benign	0.67
PhyloP100		-1.7
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: rs5749078; hg19: chr22-30761066;