rs892188

chr19-10299117-C-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 0.312 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;