rs280325

Variant names:

• chr6-50667793-A-G
• rs280325

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 0.173 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.339 AC: 14047 AN: 41458

American (AMR) AF: 0.116 AC: 1776 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3468

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5178

South Asian (SAS) AF: 0.122 AC: 590 AN: 4818

European-Finnish (FIN) AF: 0.0994 AC: 1054 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7708 AN: 68004

Other (OTH) AF: 0.157 AC: 331 AN: 2114

Alfa AF: 0.138 Hom.: 1267

Bravo AF: 0.182

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs280325; hg19: chr6-50635506;