rs4272382

Variant names:

• chr8-8575978-G-A
• rs4272382

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 0.0701 in 152,092 control chromosomes in the GnomAD database, including 626 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 0.070 (626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785

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 (EAS) allele frequency at 95% confidence interval = 0.249 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: 0.0701 AC: 10654 AN: 151972 Hom.: 623 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0701 AC: 10669 AN: 152092 Hom.: 626 Cov.: 32 AF XY: 0.0746 AC XY: 5549 AN XY: 74348

Gnomad4 AFR AF: 0.0568

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.0866

Gnomad4 FIN AF: 0.0656

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0566 Hom.: 157

Bravo AF: 0.0757

Asia WGS AF: 0.171 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4272382; hg19: chr8-8433488;