NM_025059.4:c.57+17348G>A

Variant names:

• chr6-151511533-G-A
• rs9371528
• NM_025059.4:c.57+17348G>A

Variant summary

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

The NM_025059.4(CCDC170):​c.57+17348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,086 control chromosomes in the GnomAD database, including 2,444 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 0.17 (2444 hom., cov: 32)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 3 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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.57+17348G>A		intron_variant	Intron 1 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_047419372.1	c.57+17348G>A		intron_variant	Intron 1 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.57+17348G>A		intron_variant	Intron 1 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25370 AN: 151968 Hom.: 2441 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.167 AC: 25405 AN: 152086 Hom.: 2444 Cov.: 32 AF XY: 0.168 AC XY: 12483 AN XY: 74340

African (AFR) AF: 0.219 AC: 9075 AN: 41452

American (AMR) AF: 0.138 AC: 2102 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2000 AN: 5160

South Asian (SAS) AF: 0.236 AC: 1141 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1112 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8792 AN: 68006

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.147 Hom.: 8067

Bravo AF: 0.171

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	9.2
DANN	Benign	0.93
PhyloP100		1.3
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: rs9371528; hg19: chr6-151832668;