chr7-77934500-A-T

Position:

• chr7-77934500-A-T

Variant summary

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

The ENST00000248550.7(PHTF2):​c.1339-3210A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,180 control chromosomes in the GnomAD database, including 43,768 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 0.76 (43768 hom., cov: 33)
• Consequence: PHTF2 ENST00000248550.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHTF2	NM_001395272.1	c.1237-3210A>T		intron_variant		ENST00000422959.8	NP_001382201.1
PHTF2	XM_011516422.4	c.1237-3210A>T		intron_variant			XP_011514724.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHTF2	ENST00000422959.8	c.1237-3210A>T		intron_variant		5	NM_001395272.1	ENSP00000403042	A1

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115046 AN: 152062 Hom.: 43726 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.757 AC: 115144 AN: 152180 Hom.: 43768 Cov.: 33 AF XY: 0.759 AC XY: 56488 AN XY: 74408

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.748

Alfa AF: 0.745 Hom.: 4959

Bravo AF: 0.761

Asia WGS AF: 0.770 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.1
DANN	Benign	0.49

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: rs1636665; hg19: chr7-77563817;