rs8101416

Variant names:

• chr19-5792463-A-T
• rs8101416

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 0.211 in 152,032 control chromosomes in the GnomAD database, including 3,790 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 0.21 (3790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.211 AC: 32017 AN: 151914 Hom.: 3783 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.211 AC: 32065 AN: 152032 Hom.: 3790 Cov.: 32 AF XY: 0.218 AC XY: 16225 AN XY: 74340

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.205

Alfa AF: 0.177 Hom.: 304

Bravo AF: 0.209

Asia WGS AF: 0.412 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8101416; hg19: chr19-5792474;