rs12721025

Variant names:

• chr11-116835331-G-A
• rs12721025

Your query was ambiguous. Multiple possible variants found:

• chr11-116835331-G-A
• chr11-116835331-G-C

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 0.0486 in 152,322 control chromosomes in the GnomAD database, including 250 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 0.049 (250 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0893 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: 0.0487 AC: 7408 AN: 152204 Hom.: 250 Cov.: 33

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0486 AC: 7397 AN: 152322 Hom.: 250 Cov.: 33 AF XY: 0.0493 AC XY: 3673 AN XY: 74492

Gnomad4 AFR AF: 0.0152

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0587

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0527 Hom.: 30

Bravo AF: 0.0444

Asia WGS AF: 0.0770 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12721025; hg19: chr11-116706047;