6-151589769-T-C

Position:

• chr6-151589769-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.1294-3338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,980 control chromosomes in the GnomAD database, including 23,251 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 0.49 (23251 hom., cov: 31)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC170	NM_025059.4	c.1294-3338T>C		intron_variant		ENST00000239374.8
CCDC170	XM_011536147.3	c.1312-3338T>C		intron_variant
CCDC170	XM_011536148.3	c.1111-3338T>C		intron_variant
CCDC170	XM_047419372.1	c.1093-3338T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC170	ENST00000239374.8	c.1294-3338T>C		intron_variant		1	NM_025059.4	P1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75032 AN: 151862 Hom.: 23186 Cov.: 31

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.495 AC: 75161 AN: 151980 Hom.: 23251 Cov.: 31 AF XY: 0.499 AC XY: 37097 AN XY: 74292

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.482

Alfa AF: 0.331 Hom.: 4752

Bravo AF: 0.520

Asia WGS AF: 0.648 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.76

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: rs6925996; hg19: chr6-151910904;