rs11711054

chr3-46304120-G-Achr3-46304120-G-C

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 0.726 in 152,100 control chromosomes in the GnomAD database, including 40,354 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 0.73 (40354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.726 AC: 110313 AN: 151982 Hom.: 40298 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.726 AC: 110419 AN: 152100 Hom.: 40354 Cov.: 32 AF XY: 0.722 AC XY: 53708 AN XY: 74340

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.709

Alfa AF: 0.708 Hom.: 15363

Bravo AF: 0.731

Asia WGS AF: 0.706 AC: 2453 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.93
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11711054; hg19: chr3-46345611;