rs806022

Variant names:

• chr19-50901931-C-A
• rs806022

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.317 AC: 13081 AN: 41320

American (AMR) AF: 0.457 AC: 6967 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3470

East Asian (EAS) AF: 0.0513 AC: 265 AN: 5166

South Asian (SAS) AF: 0.318 AC: 1528 AN: 4812

European-Finnish (FIN) AF: 0.511 AC: 5337 AN: 10450

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.482 AC: 32704 AN: 67894

Other (OTH) AF: 0.426 AC: 898 AN: 2108

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs806022; hg19: chr19-51405187;