6-151547655-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_025059.4(CCDC170):​c.589-649C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,886 control chromosomes in the GnomAD database, including 30,413 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 0.61 ( 30413 hom., cov: 30)

Consequence

CCDC170
NM_025059.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.99
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC170NM_025059.4 linkuse as main transcriptc.589-649C>T intron_variant ENST00000239374.8 NP_079335.2 Q8IYT3
CCDC170XM_011536147.3 linkuse as main transcriptc.607-649C>T intron_variant XP_011534449.1
CCDC170XM_011536148.3 linkuse as main transcriptc.607-649C>T intron_variant XP_011534450.1
CCDC170XM_047419372.1 linkuse as main transcriptc.589-649C>T intron_variant XP_047275328.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC170ENST00000239374.8 linkuse as main transcriptc.589-649C>T intron_variant 1 NM_025059.4 ENSP00000239374.6 Q8IYT3

Frequencies

GnomAD3 genomes
AF:
0.608
AC:
92348
AN:
151768
Hom.:
30409
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.339
Gnomad AMI
AF:
0.825
Gnomad AMR
AF:
0.723
Gnomad ASJ
AF:
0.645
Gnomad EAS
AF:
0.671
Gnomad SAS
AF:
0.684
Gnomad FIN
AF:
0.787
Gnomad MID
AF:
0.627
Gnomad NFE
AF:
0.703
Gnomad OTH
AF:
0.618
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.608
AC:
92372
AN:
151886
Hom.:
30413
Cov.:
30
AF XY:
0.614
AC XY:
45567
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.338
Gnomad4 AMR
AF:
0.724
Gnomad4 ASJ
AF:
0.645
Gnomad4 EAS
AF:
0.672
Gnomad4 SAS
AF:
0.682
Gnomad4 FIN
AF:
0.787
Gnomad4 NFE
AF:
0.703
Gnomad4 OTH
AF:
0.614
Alfa
AF:
0.674
Hom.:
15579
Bravo
AF:
0.595
Asia WGS
AF:
0.658
AC:
2289
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.32
DANN
Benign
0.67

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.

Other links and lift over

dbSNP: rs9383922; hg19: chr6-151868790; API