rs8111989

Variant names:

• chr19-45305950-T-C
• rs8111989

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 0.35 in 151,846 control chromosomes in the GnomAD database, including 10,056 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 0.35 (10056 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

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 (AFR) allele frequency at 95% confidence interval = 0.492 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: 0.350 AC: 53100 AN: 151728 Hom.: 10039 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.350 AC: 53149 AN: 151846 Hom.: 10056 Cov.: 31 AF XY: 0.348 AC XY: 25856 AN XY: 74214

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.327

Alfa AF: 0.326 Hom.: 4742

Bravo AF: 0.345

Asia WGS AF: 0.292 AC: 1019 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8111989; hg19: chr19-45809208;