chr8-19892372-A-T

Variant names:

• chr8-19892372-A-T
• rs17091651

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 0.1 in 152,236 control chromosomes in the GnomAD database, including 1,132 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 0.10 (1132 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 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: 0.101 AC: 15288 AN: 152118 Hom.: 1129 Cov.: 33

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.100 AC: 15290 AN: 152236 Hom.: 1132 Cov.: 33 AF XY: 0.105 AC XY: 7845 AN XY: 74438

African (AFR) AF: 0.0258 AC: 1071 AN: 41556

American (AMR) AF: 0.207 AC: 3165 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1551 AN: 5168

South Asian (SAS) AF: 0.125 AC: 604 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10616

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6976 AN: 67998

Other (OTH) AF: 0.109 AC: 230 AN: 2108

Alfa AF: 0.0279 Hom.: 22

Bravo AF: 0.107

Asia WGS AF: 0.179 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.42
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs17091651; hg19: chr8-19749883;