chr1-156227589-C-T

Position:

• chr1-156227589-C-T

Variant summary

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

The NM_007221.4(PMF1):​c.162-4731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 149,198 control chromosomes in the GnomAD database, including 7,902 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 0.32 (7902 hom., cov: 25)
• Consequence: PMF1 NM_007221.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

PMF1 (HGNC:9112): (polyamine modulated factor 1) Enables leucine zipper domain binding activity and transcription coactivator activity. Involved in chromosome segregation. Located in Golgi apparatus; kinetochore; and nucleoplasm. Part of MIS12/MIND type complex. Implicated in bladder carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

PMF1-BGLAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PMF1	NM_007221.4	c.162-4731C>T		intron_variant		ENST00000368277.3
PMF1-BGLAP	NM_001199662.1	c.162-4731C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PMF1	ENST00000368277.3	c.162-4731C>T		intron_variant		1	NM_007221.4	P1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48093 AN: 149086 Hom.: 7899 Cov.: 25

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.322 AC: 48114 AN: 149198 Hom.: 7902 Cov.: 25 AF XY: 0.321 AC XY: 23337 AN XY: 72646

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.328

Alfa AF: 0.332 Hom.: 1046

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.84
DANN	Benign	0.91

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: rs2984613; hg19: chr1-156197380;