rs1800247

chr1-156242034-T-C

Variant summary

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

The NM_001199662.1(PMF1-BGLAP):c.565-519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 621,846 control chromosomes in the GnomAD database, including 14,334 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 0.21 (3273 hom., cov: 32)
  • Exomes 𝑓: 0.21 (11061 hom.)
• Consequence: PMF1-BGLAP NM_001199662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

PMF1-BGLAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PMF1-BGLAP	NM_001199662.1	c.565-519T>C		intron_variant
PMF1-BGLAP	NM_001199661.1	c.504-519T>C		intron_variant
PMF1-BGLAP	NM_001199663.1	c.369-519T>C		intron_variant
PMF1-BGLAP	NM_001199664.1	c.358-519T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31290 AN: 151796 Hom.: 3273 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.213 AC: 99983 AN: 469930 Hom.: 11061 Cov.: 5 AF XY: 0.215 AC XY: 52566 AN XY: 244664

Gnomad4 AFR exome AF: 0.197

Gnomad4 AMR exome AF: 0.185

Gnomad4 ASJ exome AF: 0.223

Gnomad4 EAS exome AF: 0.239

Gnomad4 SAS exome AF: 0.237

Gnomad4 FIN exome AF: 0.153

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.218

GnomAD4 genome AF: 0.206 AC: 31286 AN: 151916 Hom.: 3273 Cov.: 32 AF XY: 0.202 AC XY: 15005 AN XY: 74248

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.220

Alfa AF: 0.208 Hom.: 969

Bravo AF: 0.211

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	1.8
Dann	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1800247; hg19: chr1-156211825; COSMIC: COSV52744978; COSMIC: COSV52744978;