rs4272382

chr8-8575978-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;