rs4128269

chr8-83822486-C-Achr8-83822486-C-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 0.195 in 152,072 control chromosomes in the GnomAD database, including 3,303 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 0.19 (3303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 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: 0.195 AC: 29615 AN: 151954 Hom.: 3300 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0917

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.195 AC: 29636 AN: 152072 Hom.: 3303 Cov.: 33 AF XY: 0.188 AC XY: 14002 AN XY: 74358

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.178

Alfa AF: 0.175 Hom.: 323

Bravo AF: 0.199

Asia WGS AF: 0.0830 AC: 286 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128269; hg19: chr8-84734721;