rs286007

chr5-56408349-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;