rs12418774

Variant names:

• chr11-68006761-A-G
• rs12418774

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 0.084 in 152,122 control chromosomes in the GnomAD database, including 686 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 0.084 (686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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: 0.0840 AC: 12774 AN: 152004 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.0840 AC: 12775 AN: 152122 Hom.: 686 Cov.: 32 AF XY: 0.0808 AC XY: 6012 AN XY: 74384

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.0806

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0666

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0951

Alfa AF: 0.103 Hom.: 458

Bravo AF: 0.0825

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12418774; hg19: chr11-67774231;