11-2212863-T-C

Variant names:

• chr11-2212863-T-C
• rs11043143

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 0.767 in 152,122 control chromosomes in the GnomAD database, including 45,000 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 0.77 (45000 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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: 0.767 AC: 116603 AN: 152004 Hom.: 44983 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.767 AC: 116668 AN: 152122 Hom.: 45000 Cov.: 33 AF XY: 0.766 AC XY: 56942 AN XY: 74356

African (AFR) AF: 0.697 AC: 28905 AN: 41486

American (AMR) AF: 0.750 AC: 11467 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4593 AN: 5148

South Asian (SAS) AF: 0.763 AC: 3679 AN: 4820

European-Finnish (FIN) AF: 0.740 AC: 7828 AN: 10584

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55030 AN: 68004

Other (OTH) AF: 0.800 AC: 1691 AN: 2114

Alfa AF: 0.800 Hom.: 20701

Bravo AF: 0.764

Asia WGS AF: 0.797 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.30
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11043143; hg19: chr11-2234093;