rs266882

chr19-50854757-G-A

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 0.48 in 151,882 control chromosomes in the GnomAD database, including 18,191 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 0.48 (18191 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72895 AN: 151764 Hom.: 18181 Cov.: 30

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.480 AC: 72935 AN: 151882 Hom.: 18191 Cov.: 30 AF XY: 0.477 AC XY: 35399 AN XY: 74264

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.459

Alfa AF: 0.467 Hom.: 5377

Bravo AF: 0.469

Asia WGS AF: 0.288 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	13
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266882; hg19: chr19-51358013;