NM_025059.4:c.*278T>C

Variant names:

• chr6-151618425-T-C
• rs6932260
• NM_025059.4:c.*278T>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.*278T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 417,186 control chromosomes in the GnomAD database, including 59,843 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 0.56 (25469 hom., cov: 32)
  • Exomes 𝑓: 0.50 (34374 hom.)
• Consequence: CCDC170 NM_025059.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 22 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 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.*278T>C		3_prime_UTR	Exon 11 of 11	NP_079335.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.*278T>C		3_prime_UTR	Exon 11 of 11	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85718 AN: 151890 Hom.: 25437 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.579

GnomAD4 exome AF: 0.504 AC: 133765 AN: 265178 Hom.: 34374 Cov.: 2 AF XY: 0.505 AC XY: 70186 AN XY: 138886

African (AFR) AF: 0.745 AC: 6415 AN: 8614

American (AMR) AF: 0.379 AC: 3614 AN: 9532

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 5116 AN: 8848

East Asian (EAS) AF: 0.391 AC: 7416 AN: 18976

South Asian (SAS) AF: 0.496 AC: 11099 AN: 22370

European-Finnish (FIN) AF: 0.451 AC: 7191 AN: 15940

Middle Eastern (MID) AF: 0.587 AC: 686 AN: 1168

European-Non Finnish (NFE) AF: 0.511 AC: 83899 AN: 164114

Other (OTH) AF: 0.533 AC: 8329 AN: 15616

GnomAD4 genome AF: 0.564 AC: 85792 AN: 152008 Hom.: 25469 Cov.: 32 AF XY: 0.556 AC XY: 41320 AN XY: 74296

African (AFR) AF: 0.751 AC: 31137 AN: 41470

American (AMR) AF: 0.433 AC: 6617 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1972 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2155 AN: 5172

South Asian (SAS) AF: 0.497 AC: 2390 AN: 4808

European-Finnish (FIN) AF: 0.451 AC: 4744 AN: 10530

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35055 AN: 67980

Other (OTH) AF: 0.582 AC: 1229 AN: 2112

Alfa AF: 0.533 Hom.: 35326

Bravo AF: 0.570

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.54
PhyloP100		-0.39
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: rs6932260; hg19: chr6-151939560;