rs1090649

Variant names:

• chr19-50903275-C-G
• rs1090649

Your query was ambiguous. Multiple possible variants found:

• chr19-50903275-C-G
• chr19-50903275-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 0.847 in 152,036 control chromosomes in the GnomAD database, including 55,717 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 0.85 (55717 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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: 0.847 AC: 128638 AN: 151916 Hom.: 55673 Cov.: 29

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.847 AC: 128743 AN: 152036 Hom.: 55717 Cov.: 29 AF XY: 0.842 AC XY: 62562 AN XY: 74290

African (AFR) AF: 0.929 AC: 38539 AN: 41486

American (AMR) AF: 0.831 AC: 12705 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1167 AN: 5146

South Asian (SAS) AF: 0.750 AC: 3600 AN: 4802

European-Finnish (FIN) AF: 0.830 AC: 8754 AN: 10550

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57950 AN: 67990

Other (OTH) AF: 0.862 AC: 1818 AN: 2108

Alfa AF: 0.852 Hom.: 6505

Bravo AF: 0.848

Asia WGS AF: 0.533 AC: 1858 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1090649; hg19: chr19-51406531;