rs1090648

Variant names:

• chr19-50903357-A-G
• rs1090648

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 0.397 in 151,668 control chromosomes in the GnomAD database, including 13,094 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 0.40 (13094 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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: 0.397 AC: 60130 AN: 151550 Hom.: 13099 Cov.: 30

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.397 AC: 60148 AN: 151668 Hom.: 13094 Cov.: 30 AF XY: 0.397 AC XY: 29380 AN XY: 74082

African (AFR) AF: 0.247 AC: 10220 AN: 41358

American (AMR) AF: 0.450 AC: 6856 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3468

East Asian (EAS) AF: 0.0519 AC: 266 AN: 5122

South Asian (SAS) AF: 0.316 AC: 1514 AN: 4792

European-Finnish (FIN) AF: 0.509 AC: 5332 AN: 10482

Middle Eastern (MID) AF: 0.465 AC: 134 AN: 288

European-Non Finnish (NFE) AF: 0.481 AC: 32683 AN: 67904

Other (OTH) AF: 0.415 AC: 873 AN: 2106

Alfa AF: 0.441 Hom.: 1983

Bravo AF: 0.385

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1090648; hg19: chr19-51406613;