rs13104799

Variant names:

• chr4-109333984-A-G
• rs13104799

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 0.274 in 152,132 control chromosomes in the GnomAD database, including 8,197 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 0.27 (8197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 0.274 AC: 41646 AN: 152012 Hom.: 8168 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.274 AC: 41731 AN: 152132 Hom.: 8197 Cov.: 32 AF XY: 0.265 AC XY: 19726 AN XY: 74382

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.228

Alfa AF: 0.196 Hom.: 4708

Bravo AF: 0.292

Asia WGS AF: 0.121 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.085
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13104799; hg19: chr4-110255140;