rs9383935

chr6-151618713-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_025059.4(CCDC170):c.*566C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 155,362 control chromosomes in the GnomAD database, including 596 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (589 hom., cov: 32)
  • Exomes 𝑓: 0.054 (7 hom.)
• Consequence: CCDC170 NM_025059.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.303

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 6-151618713-C-T is Benign according to our data. Variant chr6-151618713-C-T is described in ClinVar as [Benign]. Clinvar id is 1263708.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC170	NM_025059.4	c.*566C>T		3_prime_UTR_variant	11/11	ENST00000239374.8
CCDC170	XM_011536147.3	c.*566C>T		3_prime_UTR_variant	11/11
CCDC170	XM_011536148.3	c.*566C>T		3_prime_UTR_variant	10/10
CCDC170	XM_047419372.1	c.*566C>T		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC170	ENST00000239374.8	c.*566C>T		3_prime_UTR_variant	11/11	1	NM_025059.4	P1

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11064 AN: 152098 Hom.: 590 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.0918

GnomAD4 exome AF: 0.0537 AC: 169 AN: 3146 Hom.: 7 Cov.: 0 AF XY: 0.0560 AC XY: 92 AN XY: 1644

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0419

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.273

Gnomad4 SAS exome AF: 0.0679

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0529

Gnomad4 OTH exome AF: 0.0532

GnomAD4 genome AF: 0.0727 AC: 11062 AN: 152216 Hom.: 589 Cov.: 32 AF XY: 0.0714 AC XY: 5313 AN XY: 74424

Gnomad4 AFR AF: 0.0451

Gnomad4 AMR AF: 0.0708

Gnomad4 ASJ AF: 0.0962

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.0679

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0815 Hom.: 566

Bravo AF: 0.0767

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 17, 2020

This variant is associated with the following publications: (PMID: 25116933) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.5
Dann	Benign	0.56

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: rs9383935; hg19: chr6-151939848;