chr11-104335153-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723879	XR_001748077.2	n.127-1663C>T		intron_variant	Intron 1 of 2
LOC102723879	XR_428991.3	n.127-1663C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308576	ENST00000835153.1	n.152-1663C>T		intron_variant	Intron 1 of 2
ENSG00000308576	ENST00000835154.1	n.289-1663C>T		intron_variant	Intron 2 of 3
ENSG00000308576	ENST00000835155.1	n.314-1663C>T		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs2087324; hg19: chr11-104205881;