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. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0152 AC: 633 AN: 41594

American (AMR) AF: 0.0364 AC: 557 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.0587 AC: 304 AN: 5182

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4826

European-Finnish (FIN) AF: 0.0732 AC: 777 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0613 AC: 4170 AN: 68012

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0569 Hom.: 334

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12721025; hg19: chr11-116706047;