rs1490728

Variant names:

• chr12-18882628-G-A
• rs1490728

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.140 AC: 5797 AN: 41442

American (AMR) AF: 0.551 AC: 8405 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2425 AN: 5150

South Asian (SAS) AF: 0.659 AC: 3174 AN: 4814

European-Finnish (FIN) AF: 0.746 AC: 7894 AN: 10580

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50998 AN: 67966

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1490728; hg19: chr12-19035562;