6-151616544-C-T

Position:

• chr6-151616544-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.1947+865C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0335 in 151,980 control chromosomes in the GnomAD database, including 508 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 0.033 (508 hom., cov: 31)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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]

LOC107986528 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1947+865C>T		intron_variant		ENST00000239374.8	NP_079335.2
LOC107986528	XR_001743865.2	n.105+177G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1947+865C>T		intron_variant		1	NM_025059.4	ENSP00000239374	P1

Frequencies

GnomAD3 genomes AF: 0.0334 AC: 5068 AN: 151862 Hom.: 500 Cov.: 31

Gnomad AFR AF: 0.00457

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00338

Gnomad OTH AF: 0.0345

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

GnomAD4 genome AF: 0.0335 AC: 5088 AN: 151980 Hom.: 508 Cov.: 31 AF XY: 0.0404 AC XY: 3002 AN XY: 74286

Gnomad4 AFR AF: 0.00456

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.0981

Gnomad4 FIN AF: 0.0280

Gnomad4 NFE AF: 0.00338

Gnomad4 OTH AF: 0.0370

Alfa AF: 0.00585 Hom.: 13

Bravo AF: 0.0408

Asia WGS AF: 0.217 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.26
DANN	Benign	0.81

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: rs79692348; hg19: chr6-151937679;