rs12418774

chr11-68006761-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;