rs286007

Variant names:

• chr5-56408349-A-G
• rs286007

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 0.371 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.568 AC: 23507 AN: 41414

American (AMR) AF: 0.260 AC: 3980 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1341 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1316 AN: 5172

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3261 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20194 AN: 67988

Other (OTH) AF: 0.378 AC: 797 AN: 2110

Alfa AF: 0.317 Hom.: 32917

Bravo AF: 0.375

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.40
PhyloP100		-0.43

Splicing

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

Other links and lift over

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