chr4-99363991-G-A

Position:

• chr4-99363991-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 0.314 in 151,904 control chromosomes in the GnomAD database, including 8,905 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 (8905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47692 AN: 151786 Hom.: 8898 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0823

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.314 AC: 47715 AN: 151904 Hom.: 8905 Cov.: 32 AF XY: 0.315 AC XY: 23386 AN XY: 74272

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0819

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.288

Alfa AF: 0.372 Hom.: 1575

Bravo AF: 0.288

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154435; hg19: chr4-100285148;