11-130554931-A-G

Position:

• chr11-130554931-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 0.0952 in 152,264 control chromosomes in the GnomAD database, including 774 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 0.095 (774 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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: 0.0952 AC: 14482 AN: 152148 Hom.: 772 Cov.: 33

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0952 AC: 14494 AN: 152264 Hom.: 774 Cov.: 33 AF XY: 0.0974 AC XY: 7248 AN XY: 74452

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.0965

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0991

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.100 Hom.: 1121

Bravo AF: 0.0928

Asia WGS AF: 0.192 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11222164; hg19: chr11-130424826;