4-827765-A-G

Position:

• chr4-827765-A-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 0.526 in 151,462 control chromosomes in the GnomAD database, including 21,107 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 0.53 (21107 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79644 AN: 151346 Hom.: 21084 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.526 AC: 79703 AN: 151462 Hom.: 21107 Cov.: 31 AF XY: 0.523 AC XY: 38658 AN XY: 73972

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.545

Alfa AF: 0.518 Hom.: 2984

Bravo AF: 0.523

Asia WGS AF: 0.612 AC: 2127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11248047; hg19: chr4-821553;