rs286007

Variant names:

• chr5-56408349-A-G
• rs286007

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 0.371 in 152,040 control chromosomes in the GnomAD database, including 11,651 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 0.37 (11651 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.371 AC: 56300 AN: 151922 Hom.: 11624 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.371 AC: 56369 AN: 152040 Hom.: 11651 Cov.: 32 AF XY: 0.370 AC XY: 27534 AN XY: 74340

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.378

Alfa AF: 0.306 Hom.: 14976

Bravo AF: 0.375

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs286007; hg19: chr5-55704176; COSMIC: COSV60134763;