chr11-2052683-A-G

Variant names:

• chr11-2052683-A-G
• rs7925515
• ENST00000796724.1:n.321+12033A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000796724.1(ENSG00000303720):​n.321+12033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,414 control chromosomes in the GnomAD database, including 48,509 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 0.80 (48509 hom., cov: 28)
• Consequence: ENSG00000303720 ENST00000796724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849
• Publications: 5 publications found

Genes affected

ENSG00000303720 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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
ENSG00000303720	ENST00000796724.1	n.321+12033A>G		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796725.1	n.298+12033A>G		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796726.1	n.298+12033A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.798 AC: 120690 AN: 151298 Hom.: 48450 Cov.: 28

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.798 AC: 120808 AN: 151414 Hom.: 48509 Cov.: 28 AF XY: 0.794 AC XY: 58676 AN XY: 73944

African (AFR) AF: 0.898 AC: 37117 AN: 41354

American (AMR) AF: 0.827 AC: 12569 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2777 AN: 3458

East Asian (EAS) AF: 0.593 AC: 3035 AN: 5116

South Asian (SAS) AF: 0.686 AC: 3288 AN: 4796

European-Finnish (FIN) AF: 0.740 AC: 7750 AN: 10476

Middle Eastern (MID) AF: 0.705 AC: 203 AN: 288

European-Non Finnish (NFE) AF: 0.763 AC: 51674 AN: 67720

Other (OTH) AF: 0.798 AC: 1672 AN: 2096

Alfa AF: 0.773 Hom.: 172812

Bravo AF: 0.811

Asia WGS AF: 0.676 AC: 2350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.48
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs7925515; hg19: chr11-2073913;