rs428609

Variant names:

• chr6-94313093-A-G
• rs428609

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 0.132 in 152,028 control chromosomes in the GnomAD database, including 2,118 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 0.13 (2118 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.132 AC: 20051 AN: 151910 Hom.: 2100 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.132 AC: 20103 AN: 152028 Hom.: 2118 Cov.: 32 AF XY: 0.129 AC XY: 9602 AN XY: 74314

African (AFR) AF: 0.297 AC: 12284 AN: 41380

American (AMR) AF: 0.0838 AC: 1281 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5178

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4826

European-Finnish (FIN) AF: 0.0391 AC: 414 AN: 10584

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4730 AN: 67992

Other (OTH) AF: 0.119 AC: 252 AN: 2114

Alfa AF: 0.106 Hom.: 173

Bravo AF: 0.143

Asia WGS AF: 0.0990 AC: 347 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.26
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs428609; hg19: chr6-95022811; COSMIC: COSV69413951;