rs3025090

Positions:

• chr11-102844152-G-A

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 0.0784 in 152,188 control chromosomes in the GnomAD database, including 516 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 0.078 (516 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0902 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: 0.0784 AC: 11922 AN: 152070 Hom.: 515 Cov.: 33

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0784 AC: 11928 AN: 152188 Hom.: 516 Cov.: 33 AF XY: 0.0771 AC XY: 5733 AN XY: 74388

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.0679

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0616

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0826 Hom.: 72

Bravo AF: 0.0783

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3025090; hg19: chr11-102714883;