rs280325

chr6-50667793-A-G

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 0.173 in 152,130 control chromosomes in the GnomAD database, including 3,051 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 0.17 (3051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26289 AN: 152012 Hom.: 3039 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.173 AC: 26339 AN: 152130 Hom.: 3051 Cov.: 32 AF XY: 0.170 AC XY: 12677 AN XY: 74374

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.157

Alfa AF: 0.134 Hom.: 833

Bravo AF: 0.182

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs280325; hg19: chr6-50635506;