chr4-117039858-C-A

Variant names:

• chr4-117039858-C-A
• rs298924

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 0.614 in 151,726 control chromosomes in the GnomAD database, including 29,484 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 0.61 (29484 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744

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 (SAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93062 AN: 151608 Hom.: 29464 Cov.: 30

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.614 AC: 93110 AN: 151726 Hom.: 29484 Cov.: 30 AF XY: 0.619 AC XY: 45863 AN XY: 74144

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.561

Alfa AF: 0.645 Hom.: 63934

Bravo AF: 0.603

Asia WGS AF: 0.763 AC: 2650 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	4.8
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs298924; hg19: chr4-117961014;