rs12721025

chr11-116835331-G-Achr11-116835331-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/exons	MANE	UniProt

Ensembl

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