rs286411

Variant names:

• chr5-35559814-T-C
• rs286411

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 0.461 in 151,962 control chromosomes in the GnomAD database, including 17,502 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 0.46 (17502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.461 AC: 70034 AN: 151846 Hom.: 17500 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.461 AC: 70044 AN: 151962 Hom.: 17502 Cov.: 32 AF XY: 0.456 AC XY: 33837 AN XY: 74254

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.487

Alfa AF: 0.547 Hom.: 46936

Bravo AF: 0.450

Asia WGS AF: 0.333 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs286411; hg19: chr5-35559916;