6-151618425-T-C

Position:

• chr6-151618425-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.*278T>C		3_prime_UTR_variant	11/11	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.*278T>C		3_prime_UTR_variant	11/11		XP_011534449.1
CCDC170	XM_011536148.3	c.*278T>C		3_prime_UTR_variant	10/10		XP_011534450.1
CCDC170	XM_047419372.1	c.*278T>C		3_prime_UTR_variant	10/10		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.*278T>C		3_prime_UTR_variant	11/11	1	NM_025059.4	ENSP00000239374	P1

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

Gnomad4 AFR exome AF: 0.745

Gnomad4 AMR exome AF: 0.379

Gnomad4 ASJ exome AF: 0.578

Gnomad4 EAS exome AF: 0.391

Gnomad4 SAS exome AF: 0.496

Gnomad4 FIN exome AF: 0.451

Gnomad4 NFE exome AF: 0.511

Gnomad4 OTH exome AF: 0.533

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

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.582

Alfa AF: 0.531 Hom.: 24122

Bravo AF: 0.570

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs6932260; hg19: chr6-151939560;