rs11168839

chr12-49063852-G-A

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 0.406 in 152,068 control chromosomes in the GnomAD database, including 12,802 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 0.41 (12802 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.406 AC: 61685 AN: 151950 Hom.: 12775 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.406 AC: 61762 AN: 152068 Hom.: 12802 Cov.: 32 AF XY: 0.405 AC XY: 30102 AN XY: 74320

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.372

Alfa AF: 0.377 Hom.: 20916

Bravo AF: 0.396

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11168839; hg19: chr12-49457635;