rs11783329

Variant names:

• chr8-107883984-G-A
• rs11783329
• ENST00000665144.1:n.80+26316G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665144.1(ENSG00000287949):​n.80+26316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,926 control chromosomes in the GnomAD database, including 6,828 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 0.27 (6828 hom., cov: 31)
• Consequence: ENSG00000287949 ENST00000665144.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

Genes affected

ENSG00000287949 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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
ENSG00000287949	ENST00000665144.1	n.80+26316G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41014 AN: 151806 Hom.: 6829 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.270 AC: 41017 AN: 151926 Hom.: 6828 Cov.: 31 AF XY: 0.267 AC XY: 19844 AN XY: 74222

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.296

Alfa AF: 0.343 Hom.: 4300

Bravo AF: 0.254

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11783329; hg19: chr8-108896212;