rs12234571

Positions:

• chr7-77920589-T-G

Variant summary

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

The ENST00000422959.8(PHTF2):​c.861+124T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 692,402 control chromosomes in the GnomAD database, including 3,252 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 0.10 (1080 hom., cov: 33)
  • Exomes 𝑓: 0.076 (2172 hom.)
• Consequence: PHTF2 ENST00000422959.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHTF2	NM_001395272.1	c.861+124T>G		intron_variant		ENST00000422959.8	NP_001382201.1
PHTF2	XM_011516422.4	c.861+124T>G		intron_variant			XP_011514724.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHTF2	ENST00000422959.8	c.861+124T>G		intron_variant		5	NM_001395272.1	ENSP00000403042	A1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15453 AN: 152190 Hom.: 1077 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0764 AC: 41244 AN: 540094 Hom.: 2172 AF XY: 0.0818 AC XY: 23894 AN XY: 292006

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.0733

Gnomad4 ASJ exome AF: 0.0728

Gnomad4 EAS exome AF: 0.104

Gnomad4 SAS exome AF: 0.181

Gnomad4 FIN exome AF: 0.0286

Gnomad4 NFE exome AF: 0.0574

Gnomad4 OTH exome AF: 0.0821

GnomAD4 genome AF: 0.102 AC: 15476 AN: 152308 Hom.: 1080 Cov.: 33 AF XY: 0.102 AC XY: 7632 AN XY: 74492

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0849

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0580

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0668 Hom.: 400

Bravo AF: 0.108

Asia WGS AF: 0.182 AC: 632 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	1.5
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: rs12234571; hg19: chr7-77549906;