rs11778329

Variant names:

• chr8-48140605-C-T
• rs11778329

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 0.0797 in 152,220 control chromosomes in the GnomAD database, including 570 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 0.080 (570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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 (NFE) allele frequency at 95% confidence interval = 0.0858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12130 AN: 152102 Hom.: 569 Cov.: 32

Gnomad AFR AF: 0.0732

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0797 AC: 12134 AN: 152220 Hom.: 570 Cov.: 32 AF XY: 0.0785 AC XY: 5838 AN XY: 74406

Gnomad4 AFR AF: 0.0732

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0877

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0852 Hom.: 462

Bravo AF: 0.0804

Asia WGS AF: 0.0250 AC: 91 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	4.2
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: rs11778329; hg19: chr8-49053165;