7-77934500-A-T

Variant names:

• chr7-77934500-A-T
• rs1636665
• NM_001395272.1:c.1237-3210A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395272.1(PHTF2):​c.1237-3210A>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 NM_001395272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395272.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHTF2	NM_001395272.1	MANE Select	c.1237-3210A>T		intron	N/A	NP_001382201.1
	PHTF2	NM_001366089.1		c.1339-3210A>T		intron	N/A	NP_001353018.1
	PHTF2	NM_001127357.2		c.1237-3210A>T		intron	N/A	NP_001120829.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHTF2	ENST00000422959.8	TSL:5 MANE Select	c.1237-3210A>T		intron	N/A	ENSP00000403042.2
	PHTF2	ENST00000248550.7	TSL:1	c.1339-3210A>T		intron	N/A	ENSP00000248550.7
	PHTF2	ENST00000307305.12	TSL:1	c.1225-3210A>T		intron	N/A	ENSP00000307699.8

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

African (AFR) AF: 0.802 AC: 33282 AN: 41504

American (AMR) AF: 0.757 AC: 11570 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2595 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4442 AN: 5184

South Asian (SAS) AF: 0.706 AC: 3410 AN: 4828

European-Finnish (FIN) AF: 0.759 AC: 8040 AN: 10588

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49281 AN: 68014

Other (OTH) AF: 0.748 AC: 1580 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.1
DANN	Benign	0.49
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1636665; hg19: chr7-77563817;