Genetic Variant NM_025059.4:c.*566C>T (chr6-151618713-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.303

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4 link	c.*566C>T	3_prime_UTR_variant	Exon 11 of 11	ENST00000239374.8	NP_079335.2	Q8IYT3
CCDC170	XM_011536147.3 link	c.*566C>T	3_prime_UTR_variant	Exon 11 of 11		XP_011534449.1
CCDC170	XM_011536148.3 link	c.*566C>T	3_prime_UTR_variant	Exon 10 of 10		XP_011534450.1
CCDC170	XM_047419372.1 link	c.*566C>T	3_prime_UTR_variant	Exon 10 of 10		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8 link	c.*566C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_025059.4	ENSP00000239374.6		Q8IYT3

Frequencies

GnomAD3 genomes

AF:

0.0727

AC:

11064

AN:

152098

Hom.:

590

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.0560

AC XY:

AN XY:

1644

show subpopulations

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.:

AF XY:

0.0714

AC XY:

5313

AN XY:

74424

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 17, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over