rs298923

Variant names:

• chr4-117039490-G-A
• rs298923

Your query was ambiguous. Multiple possible variants found:

• chr4-117039490-G-A
• chr4-117039490-G-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 0.63 in 151,864 control chromosomes in the GnomAD database, including 30,733 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 0.63 (30733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• 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: 0.630 AC: 95536 AN: 151744 Hom.: 30703 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.630 AC: 95609 AN: 151864 Hom.: 30733 Cov.: 31 AF XY: 0.634 AC XY: 47077 AN XY: 74226

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.573

Alfa AF: 0.531 Hom.: 1640

Bravo AF: 0.620

Asia WGS AF: 0.767 AC: 2665 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	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs298923; hg19: chr4-117960646;