rs806287

Variant names:

• chr6-90512091-T-C
• rs806287

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 0.217 in 152,052 control chromosomes in the GnomAD database, including 4,175 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 0.22 (4175 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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: 0.217 AC: 33027 AN: 151934 Hom.: 4177 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.217 AC: 33019 AN: 152052 Hom.: 4175 Cov.: 31 AF XY: 0.217 AC XY: 16103 AN XY: 74320

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.227

Alfa AF: 0.271 Hom.: 5635

Bravo AF: 0.202

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806287; hg19: chr6-91221810; COSMIC: COSV65225762;