11-18800490-A-G

Position:

• chr11-18800490-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 0.611 in 152,020 control chromosomes in the GnomAD database, including 28,483 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 0.61 (28483 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.733 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: 0.611 AC: 92766 AN: 151902 Hom.: 28456 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.611 AC: 92835 AN: 152020 Hom.: 28483 Cov.: 31 AF XY: 0.615 AC XY: 45725 AN XY: 74292

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.587

Alfa AF: 0.610 Hom.: 38223

Bravo AF: 0.609

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4627050; hg19: chr11-18822037; COSMIC: COSV73894423;