rs280306

Variant names:

• chr6-50643622-T-A
• rs280306

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 0.177 in 151,886 control chromosomes in the GnomAD database, including 3,804 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 0.18 (3804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.176 AC: 26775 AN: 151768 Hom.: 3789 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26826 AN: 151886 Hom.: 3804 Cov.: 31 AF XY: 0.173 AC XY: 12834 AN XY: 74258

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.156

Alfa AF: 0.142 Hom.: 320

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs280306; hg19: chr6-50611335;