rs1428922

Variant names:

• chr19-41875710-A-G
• rs1428922

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 0.397 in 152,044 control chromosomes in the GnomAD database, including 13,829 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 0.40 (13829 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.563 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: 0.397 AC: 60296 AN: 151926 Hom.: 13828 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.397 AC: 60307 AN: 152044 Hom.: 13829 Cov.: 31 AF XY: 0.402 AC XY: 29855 AN XY: 74298

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.454

Alfa AF: 0.464 Hom.: 5791

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1428922; hg19: chr19-42379780;