6-151602847-T-C

Variant names:

• chr6-151602847-T-C
• rs4304175
• NM_025059.4:c.1710+6270T>C

Variant summary

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

The NM_025059.4(CCDC170):​c.1710+6270T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 150,718 control chromosomes in the GnomAD database, including 33,053 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 0.66 (33053 hom., cov: 27)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1710+6270T>C		intron_variant	Intron 9 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1728+6270T>C		intron_variant	Intron 9 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1527+6270T>C		intron_variant	Intron 8 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1509+6270T>C		intron_variant	Intron 8 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1710+6270T>C		intron_variant	Intron 9 of 10	1	NM_025059.4	ENSP00000239374.6
CCDC170	ENST00000537358.1	n.496+6270T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99177 AN: 150608 Hom.: 33044 Cov.: 27

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.658 AC: 99235 AN: 150718 Hom.: 33053 Cov.: 27 AF XY: 0.652 AC XY: 47935 AN XY: 73536

African (AFR) AF: 0.576 AC: 23572 AN: 40910

American (AMR) AF: 0.597 AC: 9066 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2381 AN: 3464

East Asian (EAS) AF: 0.543 AC: 2785 AN: 5130

South Asian (SAS) AF: 0.640 AC: 3041 AN: 4752

European-Finnish (FIN) AF: 0.691 AC: 7089 AN: 10256

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49094 AN: 67732

Other (OTH) AF: 0.662 AC: 1389 AN: 2098

Alfa AF: 0.678 Hom.: 4171

Bravo AF: 0.649

Asia WGS AF: 0.562 AC: 1952 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.18
PhyloP100		-2.3
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: rs4304175; hg19: chr6-151923982;