rs3734803

Positions:

• chr6-151548510-G-A

Variant summary

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

The NM_025059.4(CCDC170):​c.774+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,506,348 control chromosomes in the GnomAD database, including 23,435 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 0.14 (1701 hom., cov: 32)
  • Exomes 𝑓: 0.18 (21734 hom.)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

CCDC170 (HGNC:21177): (coiled-coil domain containing 170) The function of this gene and its encoded protein is not known. Several genome-wide association studies have implicated the region around this gene to be involved in breast cancer and bone mineral density, but no link to this specific gene has been found. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.774+21G>A		intron_variant		ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.792+21G>A		intron_variant			XP_011534449.1
CCDC170	XM_011536148.3	c.792+21G>A		intron_variant			XP_011534450.1
CCDC170	XM_047419372.1	c.774+21G>A		intron_variant			XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.774+21G>A		intron_variant		1	NM_025059.4	ENSP00000239374	P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21645 AN: 151842 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.163

GnomAD3 exomes AF: 0.168 AC: 34084 AN: 203220 Hom.: 2992 AF XY: 0.171 AC XY: 18959 AN XY: 111062

Gnomad AFR exome AF: 0.0845

Gnomad AMR exome AF: 0.130

Gnomad ASJ exome AF: 0.172

Gnomad EAS exome AF: 0.271

Gnomad SAS exome AF: 0.190

Gnomad FIN exome AF: 0.119

Gnomad NFE exome AF: 0.177

Gnomad OTH exome AF: 0.166

GnomAD4 exome AF: 0.177 AC: 239600 AN: 1354388 Hom.: 21734 Cov.: 29 AF XY: 0.178 AC XY: 118890 AN XY: 666456

Gnomad4 AFR exome AF: 0.0852

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.160

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.195

Gnomad4 FIN exome AF: 0.121

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.143 AC: 21659 AN: 151960 Hom.: 1701 Cov.: 32 AF XY: 0.142 AC XY: 10540 AN XY: 74282

Gnomad4 AFR AF: 0.0854

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.169

Alfa AF: 0.167 Hom.: 3164

Bravo AF: 0.143

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	6.1
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734803; hg19: chr6-151869645;