rs12150211

Positions:

• chr17-27807406-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 0.273 in 150,142 control chromosomes in the GnomAD database, including 5,829 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 0.27 (5829 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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 (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41007 AN: 150056 Hom.: 5825 Cov.: 30

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.273 AC: 41037 AN: 150142 Hom.: 5829 Cov.: 30 AF XY: 0.278 AC XY: 20361 AN XY: 73186

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.264

Alfa AF: 0.271 Hom.: 768

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12150211; hg19: chr17-26134432;