11-2086624-G-T

Variant names:

• chr11-2086624-G-T
• rs7924489
• ENST00000796724.1:n.322-924G>T

Variant summary

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

The ENST00000796724.1(ENSG00000303720):​n.322-924G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,068 control chromosomes in the GnomAD database, including 44,281 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 0.76 (44281 hom., cov: 32)
• Consequence: ENSG00000303720 ENST00000796724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796724.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303720	ENST00000796724.1		n.322-924G>T		intron	N/A
	ENSG00000303720	ENST00000796725.1		n.299-921G>T		intron	N/A
	ENSG00000303720	ENST00000796726.1		n.299-924G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115597 AN: 151950 Hom.: 44245 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.761 AC: 115689 AN: 152068 Hom.: 44281 Cov.: 32 AF XY: 0.757 AC XY: 56244 AN XY: 74318

African (AFR) AF: 0.702 AC: 29105 AN: 41476

American (AMR) AF: 0.826 AC: 12621 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2891 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2971 AN: 5156

South Asian (SAS) AF: 0.675 AC: 3251 AN: 4816

European-Finnish (FIN) AF: 0.764 AC: 8093 AN: 10588

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.797 AC: 54143 AN: 67972

Other (OTH) AF: 0.781 AC: 1643 AN: 2104

Alfa AF: 0.723 Hom.: 2709

Bravo AF: 0.764

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.21
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7924489;

hg19: chr11-2107854;