rs10215731

chr7-77860466-T-C

Variant summary

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

The ENST00000248550.7(PHTF2):c.147+5632T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,088 control chromosomes in the GnomAD database, including 4,606 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 0.24 (4606 hom., cov: 32)
• Consequence: PHTF2 ENST00000248550.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

Genes affected

PHTF2 (HGNC:13411): (putative homeodomain transcription factor 2) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHTF2	NM_001395272.1	c.45+20166T>C		intron_variant		ENST00000422959.8
PHTF2	XM_011516422.4	c.45+20166T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHTF2	ENST00000422959.8	c.45+20166T>C		intron_variant		5	NM_001395272.1	A1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37012 AN: 151970 Hom.: 4603 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.244 AC: 37041 AN: 152088 Hom.: 4606 Cov.: 32 AF XY: 0.241 AC XY: 17923 AN XY: 74344

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.237

Alfa AF: 0.252 Hom.: 6413

Bravo AF: 0.240

Asia WGS AF: 0.228 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	11
Dann	Benign	0.86

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: rs10215731; hg19: chr7-77489783;