rs1824938

Variant names:

• chr5-5091915-A-G
• rs1824938

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 0.314 in 152,108 control chromosomes in the GnomAD database, including 8,608 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 0.31 (8608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.314 AC: 47715 AN: 151990 Hom.: 8611 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.314 AC: 47714 AN: 152108 Hom.: 8608 Cov.: 32 AF XY: 0.311 AC XY: 23152 AN XY: 74346

African (AFR) AF: 0.160 AC: 6640 AN: 41522

American (AMR) AF: 0.375 AC: 5720 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.0907 AC: 470 AN: 5184

South Asian (SAS) AF: 0.319 AC: 1536 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3346 AN: 10568

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26828 AN: 67966

Other (OTH) AF: 0.361 AC: 762 AN: 2110

Alfa AF: 0.349 Hom.: 3415

Bravo AF: 0.312

Asia WGS AF: 0.195 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.81
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1824938; hg19: chr5-5092028;