rs2468475

chr5-28299109-G-Achr5-28299109-G-Cchr5-28299109-G-T

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 0.422 in 151,882 control chromosomes in the GnomAD database, including 13,929 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 0.42 (13929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

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 (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64043 AN: 151766 Hom.: 13916 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.422 AC: 64086 AN: 151882 Hom.: 13929 Cov.: 32 AF XY: 0.420 AC XY: 31177 AN XY: 74208

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.460

Alfa AF: 0.442 Hom.: 10561

Bravo AF: 0.413

Asia WGS AF: 0.282 AC: 984 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	5.6
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2468475; hg19: chr5-28299216;