11-48311808-G-A

Position:

• chr11-48311808-G-A

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 0.0957 in 152,152 control chromosomes in the GnomAD database, including 958 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 0.096 (958 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0957 AC: 14556 AN: 152034 Hom.: 958 Cov.: 33

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0353

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0957 AC: 14554 AN: 152152 Hom.: 958 Cov.: 33 AF XY: 0.0914 AC XY: 6799 AN XY: 74370

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0359

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.108

Alfa AF: 0.132 Hom.: 3309

Bravo AF: 0.0912

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1483121; hg19: chr11-48333360;