NM_025059.4:c.775-2158T>G

Variant names:

• chr6-151571016-T-G
• rs4869738
• NM_025059.4:c.775-2158T>G

Variant summary

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

The NM_025059.4(CCDC170):​c.775-2158T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 151,884 control chromosomes in the GnomAD database, including 51,335 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 0.82 (51335 hom., cov: 33)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 8 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	NM_025059.4	MANE Select	c.775-2158T>G		intron	N/A	NP_079335.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.775-2158T>G		intron	N/A	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124383 AN: 151766 Hom.: 51298 Cov.: 33

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.820 AC: 124474 AN: 151884 Hom.: 51335 Cov.: 33 AF XY: 0.821 AC XY: 60943 AN XY: 74208

African (AFR) AF: 0.889 AC: 36873 AN: 41472

American (AMR) AF: 0.824 AC: 12580 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2648 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4825 AN: 5182

South Asian (SAS) AF: 0.807 AC: 3891 AN: 4824

European-Finnish (FIN) AF: 0.827 AC: 8688 AN: 10506

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52209 AN: 67850

Other (OTH) AF: 0.802 AC: 1691 AN: 2108

Alfa AF: 0.786 Hom.: 59518

Bravo AF: 0.827

Asia WGS AF: 0.850 AC: 2951 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		1.8
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: rs4869738; hg19: chr6-151892151; COSMIC: COSV53338646;