rs892188

Variant names:

• chr19-10299117-C-T
• rs892188

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0943 AC: 3915 AN: 41496

American (AMR) AF: 0.462 AC: 7045 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1246 AN: 5154

South Asian (SAS) AF: 0.404 AC: 1944 AN: 4812

European-Finnish (FIN) AF: 0.361 AC: 3800 AN: 10532

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26804 AN: 67928

Other (OTH) AF: 0.357 AC: 753 AN: 2110

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs892188; hg19: chr19-10409793;