rs9479055

Positions:

• chr6-151526832-C-A

Variant summary

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

The NM_025059.4(CCDC170):​c.58-9486C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,836 control chromosomes in the GnomAD database, including 18,491 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 0.46 (18491 hom., cov: 30)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.58-9486C>A		intron_variant		ENST00000239374.8	NP_079335.2
CCDC170	XM_047419372.1	c.58-9486C>A		intron_variant			XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.58-9486C>A		intron_variant		1	NM_025059.4	ENSP00000239374	P1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69700 AN: 151716 Hom.: 18494 Cov.: 30

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.459 AC: 69703 AN: 151836 Hom.: 18491 Cov.: 30 AF XY: 0.455 AC XY: 33756 AN XY: 74218

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.460

Alfa AF: 0.570 Hom.: 49953

Bravo AF: 0.444

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.28

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: rs9479055; hg19: chr6-151847967; COSMIC: COSV53338303;