rs3789597

Variant names:

• chr1-113713517-C-T
• rs3789597
• NM_001323043.2:c.624-79G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHTF1	NM_001323043.2	c.624-79G>A		intron_variant	Intron 7 of 18	ENST00000369604.6	NP_001309972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHTF1	ENST00000369604.6	c.624-79G>A		intron_variant	Intron 7 of 18	5	NM_001323043.2	ENSP00000358617.1

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

African (AFR) AF: 0.568 AC: 8220 AN: 14462

American (AMR) AF: 0.196 AC: 3951 AN: 20174

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 5196 AN: 16456

East Asian (EAS) AF: 0.103 AC: 3276 AN: 31728

South Asian (SAS) AF: 0.276 AC: 14176 AN: 51280

European-Finnish (FIN) AF: 0.285 AC: 12536 AN: 44004

Middle Eastern (MID) AF: 0.254 AC: 807 AN: 3182

European-Non Finnish (NFE) AF: 0.307 AC: 114627 AN: 373056

Other (OTH) AF: 0.298 AC: 9090 AN: 30512

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

African (AFR) AF: 0.565 AC: 23423 AN: 41460

American (AMR) AF: 0.241 AC: 3679 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3468

East Asian (EAS) AF: 0.0660 AC: 341 AN: 5168

South Asian (SAS) AF: 0.261 AC: 1256 AN: 4808

European-Finnish (FIN) AF: 0.268 AC: 2823 AN: 10532

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21238 AN: 67942

Other (OTH) AF: 0.305 AC: 644 AN: 2112

Alfa AF: 0.321 Hom.: 4979

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
PhyloP100		-3.4
PromoterAI		0.0013	Neutral
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: rs3789597; hg19: chr1-114256139;