rs3789597

Positions:

• chr1-113713517-C-T

Variant summary

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

The NM_001323043.2(PHTF1):​c.624-79G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 736,806 control chromosomes in the GnomAD database, including 38,527 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 0.36 (11443 hom., cov: 32)
  • Exomes 𝑓: 0.29 (27084 hom.)
• Consequence: PHTF1 NM_001323043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

Genes affected

PHTF1 (HGNC:8939): (putative homeodomain transcription factor 1) Predicted to be located in cis-Golgi network and endoplasmic reticulum membrane. Predicted to be integral component of membrane. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHTF1	NM_001323043.2	c.624-79G>A		intron_variant		ENST00000369604.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHTF1	ENST00000369604.6	c.624-79G>A		intron_variant		5	NM_001323043.2	P1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54814 AN: 151834 Hom.: 11424 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.294 AC: 171879 AN: 584854 Hom.: 27084 Cov.: 7 AF XY: 0.293 AC XY: 90744 AN XY: 309848

Gnomad4 AFR exome AF: 0.568

Gnomad4 AMR exome AF: 0.196

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.103

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.285

Gnomad4 NFE exome AF: 0.307

Gnomad4 OTH exome AF: 0.298

GnomAD4 genome AF: 0.361 AC: 54874 AN: 151952 Hom.: 11443 Cov.: 32 AF XY: 0.355 AC XY: 26343 AN XY: 74246

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0660

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.305

Alfa AF: 0.317 Hom.: 4226

Bravo AF: 0.362

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.037
DANN	Benign	0.44

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: rs3789597; hg19: chr1-114256139;