rs9332428

chr19-28861192-G-Achr19-28861192-G-Cchr19-28861192-G-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 0.58 in 152,062 control chromosomes in the GnomAD database, including 25,684 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 0.58 (25684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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: 0.580 AC: 88115 AN: 151944 Hom.: 25654 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.580 AC: 88197 AN: 152062 Hom.: 25684 Cov.: 32 AF XY: 0.575 AC XY: 42713 AN XY: 74322

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.585

Alfa AF: 0.580 Hom.: 36481

Bravo AF: 0.590

Asia WGS AF: 0.511 AC: 1775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.1
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332428; hg19: chr19-29352099;