1-154939322-A-G

Position:

• chr1-154939322-A-G

Variant summary

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

The NM_001323012.3(PMVK):​c.-131+3254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,944 control chromosomes in the GnomAD database, including 10,945 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 0.33 (10945 hom., cov: 31)
• Consequence: PMVK NM_001323012.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

Genes affected

PMVK (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMVK	NM_001323012.3	c.-131+3254T>C		intron_variant			NP_001309941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49760 AN: 151826 Hom.: 10948 Cov.: 31

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.327 AC: 49754 AN: 151944 Hom.: 10945 Cov.: 31 AF XY: 0.338 AC XY: 25109 AN XY: 74252

Gnomad4 AFR AF: 0.0766

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.355

Alfa AF: 0.329 Hom.: 2345

Bravo AF: 0.327

Asia WGS AF: 0.652 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845695; hg19: chr1-154911798;