6-151541093-T-C

Position:

• chr6-151541093-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.443+2792T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,020 control chromosomes in the GnomAD database, including 44,126 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 0.76 (44126 hom., cov: 30)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

CCDC170 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.443+2792T>C		intron_variant		ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.461+2792T>C		intron_variant			XP_011534449.1
CCDC170	XM_011536148.3	c.461+2792T>C		intron_variant			XP_011534450.1
CCDC170	XM_047419372.1	c.443+2792T>C		intron_variant			XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.443+2792T>C		intron_variant		1	NM_025059.4	ENSP00000239374.6
CCDC170	ENST00000544131.1	n.433+2792T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115254 AN: 151900 Hom.: 44087 Cov.: 30

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.759 AC: 115348 AN: 152020 Hom.: 44126 Cov.: 30 AF XY: 0.760 AC XY: 56434 AN XY: 74304

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.728

Alfa AF: 0.715 Hom.: 45516

Bravo AF: 0.765

Asia WGS AF: 0.720 AC: 2506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs4463269; hg19: chr6-151862228; COSMIC: COSV53338447;