6-151586613-C-T

Variant names:

• chr6-151586613-C-T
• rs4869742
• NM_025059.4:c.1293+524C>T

Variant summary

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

The NM_025059.4(CCDC170):​c.1293+524C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 150,436 control chromosomes in the GnomAD database, including 16,738 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 0.44 (16738 hom., cov: 29)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 43 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025059.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	NM_025059.4	MANE Select	c.1293+524C>T		intron	N/A	NP_079335.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.1293+524C>T		intron	N/A	ENSP00000239374.6	Q8IYT3
	CCDC170	ENST00000867015.1		c.1293+524C>T		intron	N/A	ENSP00000537074.1
	CCDC170	ENST00000867016.1		c.1164+524C>T		intron	N/A	ENSP00000537075.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 65594 AN: 150318 Hom.: 16703 Cov.: 29

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.437 AC: 65690 AN: 150436 Hom.: 16738 Cov.: 29 AF XY: 0.444 AC XY: 32504 AN XY: 73198

African (AFR) AF: 0.676 AC: 27791 AN: 41116

American (AMR) AF: 0.438 AC: 6589 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1248 AN: 3454

East Asian (EAS) AF: 0.817 AC: 4182 AN: 5116

South Asian (SAS) AF: 0.462 AC: 2189 AN: 4742

European-Finnish (FIN) AF: 0.309 AC: 3102 AN: 10046

Middle Eastern (MID) AF: 0.367 AC: 105 AN: 286

European-Non Finnish (NFE) AF: 0.285 AC: 19249 AN: 67640

Other (OTH) AF: 0.444 AC: 927 AN: 2088

Alfa AF: 0.348 Hom.: 22998

Bravo AF: 0.455

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.63
PhyloP100		-1.1
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: rs4869742; hg19: chr6-151907748;