rs9292769

Variant names:

• chr5-40397809-C-T
• rs9292769

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 0.316 in 151,808 control chromosomes in the GnomAD database, including 8,198 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 0.32 (8198 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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: 0.316 AC: 47931 AN: 151690 Hom.: 8197 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.316 AC: 47944 AN: 151808 Hom.: 8198 Cov.: 31 AF XY: 0.323 AC XY: 23966 AN XY: 74156

African (AFR) AF: 0.259 AC: 10711 AN: 41400

American (AMR) AF: 0.313 AC: 4765 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3798 AN: 5148

South Asian (SAS) AF: 0.448 AC: 2157 AN: 4816

European-Finnish (FIN) AF: 0.389 AC: 4097 AN: 10532

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20490 AN: 67908

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.297 Hom.: 1275

Bravo AF: 0.307

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9292769; hg19: chr5-40397911;