rs13104799

chr4-109333984-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;