rs286411

Variant names:

• chr5-35559814-T-C
• rs286411

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.281 AC: 11635 AN: 41450

American (AMR) AF: 0.456 AC: 6955 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1792 AN: 5158

South Asian (SAS) AF: 0.346 AC: 1672 AN: 4828

European-Finnish (FIN) AF: 0.534 AC: 5624 AN: 10538

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38723 AN: 67940

Other (OTH) AF: 0.487 AC: 1030 AN: 2114

Alfa AF: 0.528 Hom.: 68487

Bravo AF: 0.450

Asia WGS AF: 0.333 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.45
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs286411; hg19: chr5-35559916;