rs428609

Positions:

• chr6-94313093-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 0.132 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

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 (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.0906

Gnomad4 FIN AF: 0.0391

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.119

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

Splicing

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

Publications

LitVar

Other links and lift over

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