rs2468475

Variant names:

• chr5-28299109-G-A
• rs2468475

Your query was ambiguous. Multiple possible variants found:

• chr5-28299109-G-A
• chr5-28299109-G-C
• chr5-28299109-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;