rs1490728

chr12-18882628-G-A

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 0.545 in 151,986 control chromosomes in the GnomAD database, including 27,823 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 0.54 (27823 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82831 AN: 151868 Hom.: 27827 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.545 AC: 82825 AN: 151986 Hom.: 27823 Cov.: 31 AF XY: 0.543 AC XY: 40363 AN XY: 74296

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.571

Alfa AF: 0.639 Hom.: 4395

Bravo AF: 0.511

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1490728; hg19: chr12-19035562;