6-151589769-T-C

Variant names:

• chr6-151589769-T-C
• rs6925996
• NM_025059.4:c.1294-3338T>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.1294-3338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,980 control chromosomes in the GnomAD database, including 23,251 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 0.49 (23251 hom., cov: 31)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1294-3338T>C		intron_variant	Intron 7 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1312-3338T>C		intron_variant	Intron 7 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1111-3338T>C		intron_variant	Intron 6 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1093-3338T>C		intron_variant	Intron 6 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1294-3338T>C		intron_variant	Intron 7 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75032 AN: 151862 Hom.: 23186 Cov.: 31

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.495 AC: 75161 AN: 151980 Hom.: 23251 Cov.: 31 AF XY: 0.499 AC XY: 37097 AN XY: 74292

African (AFR) AF: 0.860 AC: 35664 AN: 41480

American (AMR) AF: 0.458 AC: 7000 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1265 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4152 AN: 5148

South Asian (SAS) AF: 0.443 AC: 2128 AN: 4806

European-Finnish (FIN) AF: 0.340 AC: 3582 AN: 10534

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20017 AN: 67954

Other (OTH) AF: 0.482 AC: 1016 AN: 2110

Alfa AF: 0.331 Hom.: 5215

Bravo AF: 0.520

Asia WGS AF: 0.648 AC: 2254 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	7.1
DANN	Benign	0.76
PhyloP100		0.24
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: rs6925996; hg19: chr6-151910904;