rs8102754

Variant names:

• chr19-28998135-T-A
• rs8102754

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 0.49 in 151,988 control chromosomes in the GnomAD database, including 18,764 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 0.49 (18764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 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: 0.490 AC: 74365 AN: 151872 Hom.: 18754 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.490 AC: 74406 AN: 151988 Hom.: 18764 Cov.: 32 AF XY: 0.496 AC XY: 36821 AN XY: 74274

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.452

Alfa AF: 0.512 Hom.: 2476

Bravo AF: 0.474

Asia WGS AF: 0.507 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102754; hg19: chr19-29489042;