11-2874898-A-G

Position:

• chr11-2874898-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 0.692 in 152,156 control chromosomes in the GnomAD database, including 37,326 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 0.69 (37326 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2874898A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105124 AN: 152038 Hom.: 37275 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.692 AC: 105231 AN: 152156 Hom.: 37326 Cov.: 33 AF XY: 0.691 AC XY: 51428 AN XY: 74374

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.725

Alfa AF: 0.648 Hom.: 33472

Bravo AF: 0.723

Asia WGS AF: 0.808 AC: 2806 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	0.68
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2078786; hg19: chr11-2896128;