rs200502

Variant names:

• chr6-27820284-C-T
• rs200502

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 0.276 in 151,994 control chromosomes in the GnomAD database, including 6,389 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 0.28 (6389 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.276 AC: 41893 AN: 151876 Hom.: 6367 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.276 AC: 41962 AN: 151994 Hom.: 6389 Cov.: 31 AF XY: 0.272 AC XY: 20217 AN XY: 74302

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.246

Alfa AF: 0.240 Hom.: 2243

Bravo AF: 0.285

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200502; hg19: chr6-27788062;