rs286002

Variant names:

• chr5-56410642-T-C
• rs286002

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 0.274 in 151,992 control chromosomes in the GnomAD database, including 6,322 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 0.27 (6322 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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: 0.274 AC: 41649 AN: 151874 Hom.: 6313 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0676

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.274 AC: 41701 AN: 151992 Hom.: 6322 Cov.: 31 AF XY: 0.274 AC XY: 20348 AN XY: 74302

African (AFR) AF: 0.390 AC: 16154 AN: 41434

American (AMR) AF: 0.210 AC: 3206 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3468

East Asian (EAS) AF: 0.0674 AC: 348 AN: 5164

South Asian (SAS) AF: 0.205 AC: 986 AN: 4816

European-Finnish (FIN) AF: 0.243 AC: 2564 AN: 10558

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16180 AN: 67966

Other (OTH) AF: 0.294 AC: 620 AN: 2108

Alfa AF: 0.250 Hom.: 6174

Bravo AF: 0.278

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.65
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs286002; hg19: chr5-55706469; COSMIC: COSV60134809;