rs12221649

Variant names:

• chr11-114019631-T-C
• rs12221649

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 0.111 in 152,286 control chromosomes in the GnomAD database, including 1,112 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 0.11 (1112 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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 (EAS) allele frequency at 95% confidence interval = 0.186 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: 0.111 AC: 16865 AN: 152168 Hom.: 1112 Cov.: 33

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.111 AC: 16860 AN: 152286 Hom.: 1112 Cov.: 33 AF XY: 0.113 AC XY: 8443 AN XY: 74456

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.130

Alfa AF: 0.123 Hom.: 717

Bravo AF: 0.111

Asia WGS AF: 0.157 AC: 546 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	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12221649; hg19: chr11-113890353;