rs4522817

chr4-4994149-G-Achr4-4994149-G-C

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 0.492 in 149,576 control chromosomes in the GnomAD database, including 18,648 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 0.49 (18648 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 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: 0.492 AC: 73507 AN: 149462 Hom.: 18647 Cov.: 26

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.492 AC: 73522 AN: 149576 Hom.: 18648 Cov.: 26 AF XY: 0.487 AC XY: 35469 AN XY: 72804

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.475

Alfa AF: 0.542 Hom.: 27523

Bravo AF: 0.482

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.9
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4522817; hg19: chr4-4995876;