chr11-103487363-A-G

Position:

• chr11-103487363-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 0.589 in 151,894 control chromosomes in the GnomAD database, including 28,616 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 0.59 (28616 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.590 AC: 89487 AN: 151776 Hom.: 28616 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.589 AC: 89503 AN: 151894 Hom.: 28616 Cov.: 30 AF XY: 0.593 AC XY: 43980 AN XY: 74214

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.622

Alfa AF: 0.569 Hom.: 3102

Bravo AF: 0.579

Asia WGS AF: 0.668 AC: 2321 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	0.18
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895437; hg19: chr11-103358091;