rs12577147

chr11-119347938-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 0.309 in 152,080 control chromosomes in the GnomAD database, including 7,505 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 0.31 (7505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 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: 0.309 AC: 46978 AN: 151962 Hom.: 7503 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.309 AC: 46985 AN: 152080 Hom.: 7505 Cov.: 32 AF XY: 0.307 AC XY: 22852 AN XY: 74336

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.334

Alfa AF: 0.318 Hom.: 6398

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.97
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12577147; hg19: chr11-119218648;