11-79473855-A-G

Position:

• chr11-79473855-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 0.33 in 152,174 control chromosomes in the GnomAD database, including 8,401 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 0.33 (8401 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.330 AC: 50112 AN: 152052 Hom.: 8383 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.330 AC: 50179 AN: 152174 Hom.: 8401 Cov.: 33 AF XY: 0.326 AC XY: 24216 AN XY: 74396

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.317

Alfa AF: 0.341 Hom.: 4054

Bravo AF: 0.324

Asia WGS AF: 0.266 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7102569; hg19: chr11-79184899;