chr4-99366692-C-T

Position:

• chr4-99366692-C-T

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 152,044 control chromosomes in the GnomAD database, including 8,935 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 (8935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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: 47744 AN: 151928 Hom.: 8928 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.250

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: 47767 AN: 152044 Hom.: 8935 Cov.: 32 AF XY: 0.315 AC XY: 23409 AN XY: 74332

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0820

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.288

Alfa AF: 0.257 Hom.: 795

Bravo AF: 0.288

Asia WGS AF: 0.220 AC: 761 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
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: rs1154442; hg19: chr4-100287849;