rs12286898

Variant names:

• chr11-121353175-G-C
• rs12286898

Your query was ambiguous. Multiple possible variants found:

• chr11-121353175-G-C
• chr11-121353175-G-T

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 0.154 in 152,014 control chromosomes in the GnomAD database, including 2,208 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 0.15 (2208 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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: 0.154 AC: 23414 AN: 151896 Hom.: 2206 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0837

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.154 AC: 23443 AN: 152014 Hom.: 2208 Cov.: 31 AF XY: 0.154 AC XY: 11415 AN XY: 74292

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0837

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0423 Hom.: 32

Bravo AF: 0.161

Asia WGS AF: 0.149 AC: 518 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	0.78
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12286898; hg19: chr11-121223884;