rs840466

Variant names:

• chr5-122080226-A-C
• rs840466

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.857 in 151,518 control chromosomes in the GnomAD database, including 56,051 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 0.86 (56051 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 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: 0.857 AC: 129775 AN: 151400 Hom.: 55987 Cov.: 29

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.857 AC: 129897 AN: 151518 Hom.: 56051 Cov.: 29 AF XY: 0.859 AC XY: 63588 AN XY: 74022

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.836

Alfa AF: 0.824 Hom.: 10503

Bravo AF: 0.859

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840466; hg19: chr5-121415921;