chr4-99409137-G-A

Position:

• chr4-99409137-G-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 0.268 in 152,128 control chromosomes in the GnomAD database, including 5,954 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 0.27 (5954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.268 AC: 40779 AN: 152010 Hom.: 5955 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.268 AC: 40796 AN: 152128 Hom.: 5954 Cov.: 32 AF XY: 0.269 AC XY: 19974 AN XY: 74368

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.270

Alfa AF: 0.279 Hom.: 4030

Bravo AF: 0.270

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284793; hg19: chr4-100330294;