rs7753676

Variant names:

• chr6-151555680-G-A
• rs7753676
• NM_025059.4:c.774+7191G>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.774+7191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,056 control chromosomes in the GnomAD database, including 19,052 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 0.48 (19052 hom., cov: 33)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.774+7191G>A		intron_variant	Intron 5 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.792+7191G>A		intron_variant	Intron 5 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.792+7191G>A		intron_variant	Intron 5 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.774+7191G>A		intron_variant	Intron 5 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.774+7191G>A		intron_variant	Intron 5 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72296 AN: 151938 Hom.: 19057 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.475 AC: 72299 AN: 152056 Hom.: 19052 Cov.: 33 AF XY: 0.470 AC XY: 34952 AN XY: 74310

African (AFR) AF: 0.265 AC: 11007 AN: 41478

American (AMR) AF: 0.496 AC: 7577 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1771 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5160

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6394 AN: 10568

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40656 AN: 67978

Other (OTH) AF: 0.466 AC: 982 AN: 2106

Alfa AF: 0.550 Hom.: 14513

Bravo AF: 0.460

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	-0.88
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		0.73
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: rs7753676; hg19: chr6-151876815; COSMIC: COSV53345511;