rs11168839

Variant names:

• chr12-49063852-G-A
• rs11168839

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;