rs11914380

chr3-86846858-C-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 0.0586 in 150,588 control chromosomes in the GnomAD database, including 605 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 0.059 (605 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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: 0.0585 AC: 8802 AN: 150484 Hom.: 600 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0226

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.00612

Gnomad OTH AF: 0.0681

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

GnomAD4 genome AF: 0.0586 AC: 8829 AN: 150588 Hom.: 605 Cov.: 31 AF XY: 0.0611 AC XY: 4490 AN XY: 73490

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0226

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0103

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.00612

Gnomad4 OTH AF: 0.0713

Alfa AF: 0.0182 Hom.: 274

Bravo AF: 0.0752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.8
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: rs11914380; hg19: chr3-86896008;