rs3748492

Positions:

• chr20-18012625-C-T

Variant summary

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

The variant allele was found at a frequency of 0.586 in 152,168 control chromosomes in the GnomAD database, including 26,501 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 0.59 (26501 hom., cov: 34)
• Consequence: PTMAP3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.15

Genes affected

PTMAP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTMAP3		n.18012625C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OVOL2	ENST00000486776.5	n.300-15873G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89131 AN: 152050 Hom.: 26460 Cov.: 34

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.586 AC: 89215 AN: 152168 Hom.: 26501 Cov.: 34 AF XY: 0.589 AC XY: 43843 AN XY: 74386

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.586

Alfa AF: 0.563 Hom.: 15667

Bravo AF: 0.580

Asia WGS AF: 0.555 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.68
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3748492; hg19: chr20-17993269;