rs868082

Variant names:

• chr4-183359791-G-A
• rs868082

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 0.0838 in 152,184 control chromosomes in the GnomAD database, including 618 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 0.084 (618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 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: 0.0837 AC: 12735 AN: 152066 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.00944

Gnomad SAS AF: 0.0558

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0838 AC: 12750 AN: 152184 Hom.: 618 Cov.: 32 AF XY: 0.0823 AC XY: 6121 AN XY: 74380

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.00946

Gnomad4 SAS AF: 0.0556

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.0997 Hom.: 1086

Bravo AF: 0.0781

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868082; hg19: chr4-184280944;