rs12418204

Positions:

• chr11-72539079-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 0.0591 in 152,156 control chromosomes in the GnomAD database, including 263 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 0.059 (263 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.07 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: 0.0591 AC: 8993 AN: 152038 Hom.: 263 Cov.: 30

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0591 AC: 8999 AN: 152156 Hom.: 263 Cov.: 30 AF XY: 0.0592 AC XY: 4401 AN XY: 74384

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.0567

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0699

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0393

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0561 Hom.: 381

Bravo AF: 0.0607

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12418204; hg19: chr11-72250123;