4-107498658-T-G

Variant names:

• chr4-107498658-T-G
• rs1399403

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 0.733 in 152,038 control chromosomes in the GnomAD database, including 40,950 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 0.73 (40950 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 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: 0.733 AC: 111297 AN: 151920 Hom.: 40910 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.733 AC: 111393 AN: 152038 Hom.: 40950 Cov.: 32 AF XY: 0.734 AC XY: 54525 AN XY: 74312

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.733

Alfa AF: 0.706 Hom.: 75825

Bravo AF: 0.734

Asia WGS AF: 0.840 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399403; hg19: chr4-108419815;