rs2087324

Variant names:

• chr11-104335153-C-T
• rs2087324
• ENST00000835153.1:n.152-1663C>T

Variant summary

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

The ENST00000835153.1(ENSG00000308576):​n.152-1663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,782 control chromosomes in the GnomAD database, including 7,009 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 0.30 (7009 hom., cov: 32)
• Consequence: ENSG00000308576 ENST00000835153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 1 publications found

Genes affected

ENSG00000308576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835153.1. 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
	ENSG00000308576	ENST00000835153.1		n.152-1663C>T		intron	N/A
	ENSG00000308576	ENST00000835154.1		n.289-1663C>T		intron	N/A
	ENSG00000308576	ENST00000835155.1		n.314-1663C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45008 AN: 151662 Hom.: 7007 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.297 AC: 45033 AN: 151782 Hom.: 7009 Cov.: 32 AF XY: 0.296 AC XY: 21951 AN XY: 74176

African (AFR) AF: 0.206 AC: 8516 AN: 41422

American (AMR) AF: 0.315 AC: 4803 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1747 AN: 5146

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4812

European-Finnish (FIN) AF: 0.306 AC: 3210 AN: 10476

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22555 AN: 67890

Other (OTH) AF: 0.315 AC: 665 AN: 2110

Alfa AF: 0.316 Hom.: 2030

Bravo AF: 0.289

Asia WGS AF: 0.371 AC: 1285 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.69
PhyloP100		0.070

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: rs2087324;

hg19: chr11-104205881;