chr19-12890733-A-G

Variant names:

• chr19-12890733-A-G
• rs11085824

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 0.309 in 151,662 control chromosomes in the GnomAD database, including 7,755 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 0.31 (7755 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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: 0.309 AC: 46752 AN: 151544 Hom.: 7737 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.309 AC: 46805 AN: 151662 Hom.: 7755 Cov.: 30 AF XY: 0.304 AC XY: 22558 AN XY: 74108

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.325

Alfa AF: 0.355 Hom.: 18907

Bravo AF: 0.314

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11085824; hg19: chr19-13001547;