rs11116045

Variant names:

• chr12-83802750-A-G
• rs11116045

Your query was ambiguous. Multiple possible variants found:

• chr12-83802750-A-G
• chr12-83802750-A-T

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 0.281 in 152,032 control chromosomes in the GnomAD database, including 6,380 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 0.28 (6380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.281 AC: 42660 AN: 151914 Hom.: 6373 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.281 AC: 42707 AN: 152032 Hom.: 6380 Cov.: 32 AF XY: 0.279 AC XY: 20766 AN XY: 74330

African (AFR) AF: 0.379 AC: 15694 AN: 41444

American (AMR) AF: 0.264 AC: 4022 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3470

East Asian (EAS) AF: 0.127 AC: 660 AN: 5178

South Asian (SAS) AF: 0.149 AC: 717 AN: 4820

European-Finnish (FIN) AF: 0.274 AC: 2902 AN: 10582

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.251 AC: 17071 AN: 67968

Other (OTH) AF: 0.273 AC: 575 AN: 2106

Alfa AF: 0.262 Hom.: 14684

Bravo AF: 0.287

Asia WGS AF: 0.136 AC: 475 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs11116045; hg19: chr12-84196529;