rs345909

Variant names:

• chr5-93012788-A-T
• rs345909

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 0.409 in 151,908 control chromosomes in the GnomAD database, including 14,321 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 0.41 (14321 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 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: 0.409 AC: 62140 AN: 151790 Hom.: 14321 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.409 AC: 62134 AN: 151908 Hom.: 14321 Cov.: 31 AF XY: 0.401 AC XY: 29737 AN XY: 74212

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.469

Alfa AF: 0.475 Hom.: 2322

Bravo AF: 0.394

Asia WGS AF: 0.343 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs345909; hg19: chr5-92348494;