rs863820

Variant names:

• chr6-146026266-A-G
• rs863820

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 0.391 in 152,040 control chromosomes in the GnomAD database, including 11,964 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 0.39 (11964 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.391 AC: 59395 AN: 151922 Hom.: 11951 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.391 AC: 59430 AN: 152040 Hom.: 11964 Cov.: 32 AF XY: 0.393 AC XY: 29211 AN XY: 74336

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.407

Alfa AF: 0.390 Hom.: 2001

Bravo AF: 0.375

Asia WGS AF: 0.409 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.41
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs863820; hg19: chr6-146347402;