NM_001017437.5:c.151G>A

Variant names:

• chr22-30366151-G-A
• rs740223
• NM_001017437.5:c.151G>A

Variant summary

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

The NM_001017437.5(CCDC157):​c.151G>A​(p.Asp51Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,613,584 control chromosomes in the GnomAD database, including 41,813 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 0.20 (3366 hom., cov: 32)
  • Exomes 𝑓: 0.22 (38447 hom.)
• Consequence: CCDC157 NM_001017437.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.17
• Publications: 31 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 (MetaRNN=0.0016170144).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017437.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC157	NM_001017437.5	MANE Select	c.151G>A	p.Asp51Asn	missense	Exon 3 of 12	NP_001017437.3
	CCDC157	NM_001318334.2		c.151G>A	p.Asp51Asn	missense	Exon 3 of 12	NP_001305263.2
	CCDC157	NM_001318335.2		c.151G>A	p.Asp51Asn	missense	Exon 3 of 3	NP_001305264.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC157	ENST00000338306.8	TSL:5 MANE Select	c.151G>A	p.Asp51Asn	missense	Exon 3 of 12	ENSP00000343087.3
	CCDC157	ENST00000405659.5	TSL:1	c.151G>A	p.Asp51Asn	missense	Exon 3 of 12	ENSP00000385357.1
	CCDC157	ENST00000399824.6	TSL:1	c.151G>A	p.Asp51Asn	missense	Exon 3 of 3	ENSP00000382720.2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30703 AN: 152104 Hom.: 3366 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.247

GnomAD2 exomes AF: 0.197 AC: 49350 AN: 250802 AF XY: 0.199

Gnomad AFR exome AF: 0.149

Gnomad AMR exome AF: 0.141

Gnomad ASJ exome AF: 0.318

Gnomad EAS exome AF: 0.143

Gnomad FIN exome AF: 0.163

Gnomad NFE exome AF: 0.246

Gnomad OTH exome AF: 0.233

GnomAD4 exome AF: 0.224 AC: 326929 AN: 1461362 Hom.: 38447 Cov.: 35 AF XY: 0.221 AC XY: 160937 AN XY: 727028

African (AFR) AF: 0.153 AC: 5121 AN: 33480

American (AMR) AF: 0.147 AC: 6563 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 8267 AN: 26136

East Asian (EAS) AF: 0.109 AC: 4332 AN: 39700

South Asian (SAS) AF: 0.110 AC: 9522 AN: 86258

European-Finnish (FIN) AF: 0.160 AC: 8463 AN: 52936

Middle Eastern (MID) AF: 0.265 AC: 1528 AN: 5768

European-Non Finnish (NFE) AF: 0.242 AC: 269422 AN: 1111974

Other (OTH) AF: 0.227 AC: 13711 AN: 60386

GnomAD4 genome AF: 0.202 AC: 30704 AN: 152222 Hom.: 3366 Cov.: 32 AF XY: 0.195 AC XY: 14509 AN XY: 74440

African (AFR) AF: 0.153 AC: 6335 AN: 41532

American (AMR) AF: 0.209 AC: 3192 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3466

East Asian (EAS) AF: 0.135 AC: 696 AN: 5174

South Asian (SAS) AF: 0.0955 AC: 461 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1662 AN: 10610

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16465 AN: 68000

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.238 Hom.: 8501

Bravo AF: 0.207

TwinsUK AF: 0.234 AC: 866

ALSPAC AF: 0.252 AC: 971

ESP6500AA AF: 0.151 AC: 667

ESP6500EA AF: 0.256 AC: 2204

ExAC AF: 0.196 AC: 23796

Asia WGS AF: 0.130 AC: 455 AN: 3478

EpiCase AF: 0.265

EpiControl AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.48	T
BayesDel_noAF	Benign	-0.32
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.10	T
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.91	D
MetaRNN	Benign	0.0016	T
MetaSVM	Benign	-1.2	T
MutationAssessor	Uncertain	2.2	M
PhyloP100		9.2
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-3.6	D
REVEL	Uncertain	0.35
Sift	Benign	0.11	T
Sift4G	Uncertain	0.045	D
Polyphen		1.0	D
Vest4		0.79
MPC		0.46
ClinPred		0.010	T
GERP RS		5.3
Varity_R		0.16
gMVP		0.45
Mutation Taster		=92/8	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: rs740223; hg19: chr22-30762140; COSMIC: COSV57837547; COSMIC: COSV57837547;