NM_025059.4:c.1293+524C>T

Variant names:

• chr6-151586613-C-T
• rs4869742
• NM_025059.4:c.1293+524C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025059.4(CCDC170):​c.1293+524C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 150,436 control chromosomes in the GnomAD database, including 16,738 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 0.44 (16738 hom., cov: 29)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1293+524C>T		intron_variant	Intron 7 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1311+524C>T		intron_variant	Intron 7 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1111-6494C>T		intron_variant	Intron 6 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1093-6494C>T		intron_variant	Intron 6 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1293+524C>T		intron_variant	Intron 7 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.436 AC: 65594 AN: 150318 Hom.: 16703 Cov.: 29

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.437 AC: 65690 AN: 150436 Hom.: 16738 Cov.: 29 AF XY: 0.444 AC XY: 32504 AN XY: 73198

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.444

Alfa AF: 0.304 Hom.: 3567

Bravo AF: 0.455

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.63

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: rs4869742; hg19: chr6-151907748;