4-107498658-T-G

Variant names:

• chr4-107498658-T-G
• rs1399403

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.794 AC: 32923 AN: 41480

American (AMR) AF: 0.717 AC: 10964 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2361 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4177 AN: 5150

South Asian (SAS) AF: 0.822 AC: 3963 AN: 4822

European-Finnish (FIN) AF: 0.694 AC: 7315 AN: 10542

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47325 AN: 67972

Other (OTH) AF: 0.733 AC: 1549 AN: 2114

Alfa AF: 0.709 Hom.: 163720

Bravo AF: 0.734

Asia WGS AF: 0.840 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.66
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs1399403; hg19: chr4-108419815;