6-151577371-C-T

Position:

• chr6-151577371-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.1092+3880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,056 control chromosomes in the GnomAD database, including 3,121 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 0.18 (3121 hom., cov: 32)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC170	NM_025059.4	c.1092+3880C>T		intron_variant		ENST00000239374.8
CCDC170	XM_011536147.3	c.1110+3880C>T		intron_variant
CCDC170	XM_011536148.3	c.1110+3880C>T		intron_variant
CCDC170	XM_047419372.1	c.1092+3880C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC170	ENST00000239374.8	c.1092+3880C>T		intron_variant		1	NM_025059.4	P1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27969 AN: 151936 Hom.: 3120 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.184 AC: 28005 AN: 152056 Hom.: 3121 Cov.: 32 AF XY: 0.194 AC XY: 14432 AN XY: 74308

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.193

Alfa AF: 0.139 Hom.: 2448

Bravo AF: 0.191

Asia WGS AF: 0.384 AC: 1336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.69

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: rs1871859; hg19: chr6-151898506;