chr10-103341944-C-T

Position:

• chr10-103341944-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001011663.2(PCGF6):​c.782+3080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 149,212 control chromosomes in the GnomAD database, including 1,404 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 0.12 (1404 hom., cov: 30)
• Consequence: PCGF6 NM_001011663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

PCGF6 (HGNC:21156): (polycomb group ring finger 6) The protein encoded by this gene contains a RING finger motif, which is most closely related to those of polycomb group (PcG) proteins RNF110/MEL-18 and BMI1. PcG proteins are known to form protein complexes and function as transcription repressors. This protein has been shown to interact with some PcG proteins and act as a transcription repressor. The activity of this protein is found to be regulated by cell cycle dependent phosphorylation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCGF6	NM_001011663.2	c.782+3080G>A		intron_variant		ENST00000369847.4
PCGF6	NM_032154.4	c.557+6772G>A		intron_variant
PCGF6	XM_047425832.1	c.782+3080G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCGF6	ENST00000369847.4	c.782+3080G>A		intron_variant		1	NM_001011663.2	P1
PCGF6	ENST00000337211.8	c.557+6772G>A		intron_variant		1
PCGF6	ENST00000647574.1	c.*39-2175G>A		intron_variant, NMD_transcript_variant
PCGF6	ENST00000490296.1	n.819+3080G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18160 AN: 149112 Hom.: 1403 Cov.: 30

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0974

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.122 AC: 18155 AN: 149212 Hom.: 1404 Cov.: 30 AF XY: 0.119 AC XY: 8704 AN XY: 72886

Gnomad4 AFR AF: 0.0374

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.130

Alfa AF: 0.146 Hom.: 1290

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.75

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: rs11191659; hg19: chr10-105101701;