4-99323064-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 0.447 in 151,848 control chromosomes in the GnomAD database, including 15,752 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 0.45 (15752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.447 AC: 67832 AN: 151728 Hom.: 15744 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.447 AC: 67869 AN: 151848 Hom.: 15752 Cov.: 32 AF XY: 0.443 AC XY: 32894 AN XY: 74220

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.0965

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.417

Alfa AF: 0.429 Hom.: 13531

Bravo AF: 0.437

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.94
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811802; hg19: chr4-100244221;