rs806022

Positions:

• chr19-50901931-C-A
• chr19-50901931-C-T

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 0.417 in 151,678 control chromosomes in the GnomAD database, including 13,918 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 0.42 (13918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63155 AN: 151562 Hom.: 13914 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.417 AC: 63196 AN: 151678 Hom.: 13918 Cov.: 31 AF XY: 0.416 AC XY: 30838 AN XY: 74102

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.0513

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.426

Alfa AF: 0.445 Hom.: 1923

Bravo AF: 0.408

Asia WGS AF: 0.192 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806022; hg19: chr19-51405187;