rs12286898

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;