rs900195

Positions:

• chr6-151604242-C-T

Variant summary

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

The NM_025059.4(CCDC170):​c.1710+7665C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,978 control chromosomes in the GnomAD database, including 21,066 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 (21066 hom., cov: 31)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1710+7665C>T		intron_variant		ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1728+7665C>T		intron_variant			XP_011534449.1
CCDC170	XM_011536148.3	c.1527+7665C>T		intron_variant			XP_011534450.1
CCDC170	XM_047419372.1	c.1509+7665C>T		intron_variant			XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1710+7665C>T		intron_variant		1	NM_025059.4	ENSP00000239374	P1
CCDC170	ENST00000537358.1	n.496+7665C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74123 AN: 151860 Hom.: 21066 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.488 AC: 74154 AN: 151978 Hom.: 21066 Cov.: 31 AF XY: 0.486 AC XY: 36120 AN XY: 74284

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.491

Alfa AF: 0.602 Hom.: 16985

Bravo AF: 0.460

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.58

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: rs900195; hg19: chr6-151925377;