chr1-156212919-T-C

Variant names:

• chr1-156212919-T-C
• rs2241107
• ENST00000797853.1:n.277A>G

Variant summary

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

The ENST00000797853.1(ENSG00000303877):​n.277A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,559,212 control chromosomes in the GnomAD database, including 104,019 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 0.42 (14913 hom., cov: 33)
  • Exomes 𝑓: 0.35 (89106 hom.)
• Consequence: ENSG00000303877 ENST00000797853.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 16 publications found

Genes affected

ENSG00000303877 (HGNC:):

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:42953): (PMF1-BGLAP readthrough) This locus represents naturally occurring read-through transcription between the neighboring PMF1 (polyamine-modulated factor 1) and BGLAP (bone gamma-carboxyglutamate Gla protein) genes on chromosome 1. Alternative splicing results in multiple transcript variants encoding isoforms that share sequence identity with the upstream gene product, but they contain distinct C-termini due to frameshifts versus the downstream gene coding sequence. [provided by RefSeq, Dec 2010]

SLC25A44 (HGNC:29036): (solute carrier family 25 member 44) SLC25A44 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMF1	NM_007221.4	c.-97T>C		upstream_gene_variant		ENST00000368277.3	NP_009152.2
SLC25A44	NM_014655.4	c.*2488T>C		downstream_gene_variant		ENST00000359511.5	NP_055470.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMF1	ENST00000368277.3	c.-97T>C		upstream_gene_variant		1	NM_007221.4	ENSP00000357260.3
PMF1-BGLAP	ENST00000490491.5	c.-97T>C		upstream_gene_variant		2		ENSP00000475561.1
SLC25A44	ENST00000359511.5	c.*2488T>C		downstream_gene_variant		1	NM_014655.4	ENSP00000352497.4

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63754 AN: 151950 Hom.: 14870 Cov.: 33

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.352 AC: 494680 AN: 1407144 Hom.: 89106 Cov.: 27 AF XY: 0.348 AC XY: 242503 AN XY: 695970

African (AFR) AF: 0.651 AC: 21111 AN: 32452

American (AMR) AF: 0.297 AC: 12263 AN: 41308

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 7010 AN: 23096

East Asian (EAS) AF: 0.166 AC: 6232 AN: 37626

South Asian (SAS) AF: 0.296 AC: 23808 AN: 80350

European-Finnish (FIN) AF: 0.343 AC: 17138 AN: 50032

Middle Eastern (MID) AF: 0.334 AC: 1530 AN: 4576

European-Non Finnish (NFE) AF: 0.356 AC: 384946 AN: 1080188

Other (OTH) AF: 0.359 AC: 20642 AN: 57516

GnomAD4 genome AF: 0.420 AC: 63845 AN: 152068 Hom.: 14913 Cov.: 33 AF XY: 0.413 AC XY: 30700 AN XY: 74364

African (AFR) AF: 0.633 AC: 26246 AN: 41486

American (AMR) AF: 0.337 AC: 5159 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1041 AN: 3464

East Asian (EAS) AF: 0.160 AC: 826 AN: 5172

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4814

European-Finnish (FIN) AF: 0.349 AC: 3689 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24262 AN: 67956

Other (OTH) AF: 0.399 AC: 843 AN: 2112

Alfa AF: 0.290 Hom.: 993

Bravo AF: 0.427

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.36
DANN	Benign	0.60
PhyloP100		-1.6
PromoterAI		0.0052	Neutral
Mutation Taster		=82/18	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2241107; hg19: chr1-156182710;