4-99326194-C-A

Position:

• chr4-99326194-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 0.127 in 152,188 control chromosomes in the GnomAD database, including 1,518 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 0.13 (1518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 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: 0.127 AC: 19272 AN: 152070 Hom.: 1510 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.127 AC: 19286 AN: 152188 Hom.: 1518 Cov.: 32 AF XY: 0.128 AC XY: 9514 AN XY: 74392

Gnomad4 AFR AF: 0.0387

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.118

Alfa AF: 0.151 Hom.: 2482

Bravo AF: 0.120

Asia WGS AF: 0.143 AC: 494 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213041; hg19: chr4-100247351;