6-169713148-C-A

Position:

• chr6-169713148-C-A

Variant summary

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

The NM_018288.4(PHF10):​c.804-609G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,152 control chromosomes in the GnomAD database, including 2,731 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 0.17 (2731 hom., cov: 32)
• Consequence: PHF10 NM_018288.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

Genes affected

PHF10 (HGNC:18250): (PHD finger protein 10) This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known. Sequence analysis suggests that multiple alternatively spliced transcript variants are derived from this gene but the full-length nature of only two of them is known. These two splice variants encode different isoforms. A pseudogene for this gene is located on Xq28. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF10	NM_018288.4	c.804-609G>T		intron_variant		ENST00000339209.9	NP_060758.2
PHF10	NM_133325.3	c.798-609G>T		intron_variant			NP_579866.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF10	ENST00000339209.9	c.804-609G>T		intron_variant		1	NM_018288.4	ENSP00000341805

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25691 AN: 152034 Hom.: 2713 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0853

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.169 AC: 25754 AN: 152152 Hom.: 2731 Cov.: 32 AF XY: 0.169 AC XY: 12563 AN XY: 74412

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0853

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.168

Alfa AF: 0.138 Hom.: 818

Bravo AF: 0.181

Asia WGS AF: 0.286 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.63

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: rs7762018; hg19: chr6-170113244;