22-30361306-A-G

Variant names:

• chr22-30361306-A-G
• rs737950
• NM_001017437.5:c.-165-655A>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.-165-655A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 150,730 control chromosomes in the GnomAD database, including 58,075 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 (58075 hom., cov: 25)
• Consequence: CCDC157 NM_001017437.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 9 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=-1.07).
• 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.-165-655A>G		intron_variant	Intron 1 of 11	ENST00000338306.8	NP_001017437.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC157	ENST00000338306.8	c.-165-655A>G		intron_variant	Intron 1 of 11	5	NM_001017437.5	ENSP00000343087.3

Frequencies

GnomAD3 genomes AF: 0.875 AC: 131793 AN: 150616 Hom.: 58017 Cov.: 25

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.875 AC: 131906 AN: 150730 Hom.: 58075 Cov.: 25 AF XY: 0.880 AC XY: 64640 AN XY: 73458

African (AFR) AF: 0.967 AC: 39614 AN: 40970

American (AMR) AF: 0.871 AC: 13086 AN: 15028

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4615 AN: 5098

South Asian (SAS) AF: 0.922 AC: 4380 AN: 4752

European-Finnish (FIN) AF: 0.888 AC: 9128 AN: 10280

Middle Eastern (MID) AF: 0.966 AC: 282 AN: 292

European-Non Finnish (NFE) AF: 0.814 AC: 55201 AN: 67840

Other (OTH) AF: 0.879 AC: 1839 AN: 2092

Alfa AF: 0.840 Hom.: 35928

Bravo AF: 0.875

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	-1.1
CADD	Benign	0.40
DANN	Benign	0.23
PhyloP100		-2.7
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: rs737950; hg19: chr22-30757295; COSMIC: COSV53171391; COSMIC: COSV53171391;