11-2874898-A-G

Variant names:

• chr11-2874898-A-G
• rs2078786

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.777 AC: 32280 AN: 41536

American (AMR) AF: 0.800 AC: 12241 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2628 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5130 AN: 5168

South Asian (SAS) AF: 0.646 AC: 3116 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5669 AN: 10570

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.614 AC: 41770 AN: 67976

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.655 Hom.: 108957

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2078786; hg19: chr11-2896128;