chr11-102284743-A-G

Variant names:

• chr11-102284743-A-G
• rs2852894

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 0.935 in 152,240 control chromosomes in the GnomAD database, including 66,582 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 0.93 (66582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.935 AC: 142219 AN: 152122 Hom.: 66521 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.935 AC: 142339 AN: 152240 Hom.: 66582 Cov.: 32 AF XY: 0.936 AC XY: 69697 AN XY: 74430

African (AFR) AF: 0.960 AC: 39861 AN: 41538

American (AMR) AF: 0.949 AC: 14518 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3255 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5168 AN: 5188

South Asian (SAS) AF: 0.952 AC: 4593 AN: 4824

European-Finnish (FIN) AF: 0.917 AC: 9706 AN: 10590

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62162 AN: 68012

Other (OTH) AF: 0.934 AC: 1971 AN: 2110

Alfa AF: 0.924 Hom.: 142779

Bravo AF: 0.937

Asia WGS AF: 0.972 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.90
DANN	Benign	0.37
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2852894; hg19: chr11-102155474;