4-827765-A-G

Variant names:

• chr4-827765-A-G
• rs11248047

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;