rs892188

Variant names:

• chr19-10299117-C-T
• rs892188

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 0.312 in 151,966 control chromosomes in the GnomAD database, including 8,981 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 (8981 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 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: 0.312 AC: 47435 AN: 151848 Hom.: 8983 Cov.: 31

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.312 AC: 47429 AN: 151966 Hom.: 8981 Cov.: 31 AF XY: 0.314 AC XY: 23294 AN XY: 74268

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.357

Alfa AF: 0.338 Hom.: 2240

Bravo AF: 0.312

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs892188; hg19: chr19-10409793;