chr6-151526832-C-A

Variant names:

• chr6-151526832-C-A
• rs9479055
• NM_025059.4:c.58-9486C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.58-9486C>A		intron_variant	Intron 1 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_047419372.1	c.58-9486C>A		intron_variant	Intron 1 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.58-9486C>A		intron_variant	Intron 1 of 10	1	NM_025059.4	ENSP00000239374.6

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

African (AFR) AF: 0.203 AC: 8385 AN: 41376

American (AMR) AF: 0.501 AC: 7639 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1741 AN: 3462

East Asian (EAS) AF: 0.200 AC: 1033 AN: 5176

South Asian (SAS) AF: 0.451 AC: 2164 AN: 4800

European-Finnish (FIN) AF: 0.585 AC: 6150 AN: 10516

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40927 AN: 67942

Other (OTH) AF: 0.460 AC: 972 AN: 2114

Alfa AF: 0.552 Hom.: 73687

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
PhyloP100		0.046
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: rs9479055; hg19: chr6-151847967; COSMIC: COSV53338303;