rs9292903

Variant names:

• chr5-44299896-G-A
• rs9292903

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 0.284 in 151,902 control chromosomes in the GnomAD database, including 6,181 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 0.28 (6181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 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: 0.284 AC: 43110 AN: 151782 Hom.: 6183 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.284 AC: 43133 AN: 151902 Hom.: 6181 Cov.: 32 AF XY: 0.281 AC XY: 20842 AN XY: 74216

African (AFR) AF: 0.238 AC: 9870 AN: 41446

American (AMR) AF: 0.344 AC: 5234 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 987 AN: 3470

East Asian (EAS) AF: 0.171 AC: 883 AN: 5164

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4816

European-Finnish (FIN) AF: 0.297 AC: 3122 AN: 10526

Middle Eastern (MID) AF: 0.300 AC: 87 AN: 290

European-Non Finnish (NFE) AF: 0.305 AC: 20699 AN: 67940

Other (OTH) AF: 0.306 AC: 646 AN: 2108

Alfa AF: 0.300 Hom.: 6495

Bravo AF: 0.288

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.70
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs9292903; hg19: chr5-44299998;