4-99358090-C-A

Position:

• chr4-99358090-C-A

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 0.314 in 152,076 control chromosomes in the GnomAD database, including 8,922 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 0.31 (8922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.314 AC: 47714 AN: 151958 Hom.: 8915 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.314 AC: 47737 AN: 152076 Hom.: 8922 Cov.: 32 AF XY: 0.315 AC XY: 23382 AN XY: 74330

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0817

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.288

Alfa AF: 0.257 Hom.: 794

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs980972; hg19: chr4-100279247;