11-112121869-C-T

Variant names:

• chr11-112121869-C-T
• rs11214093
• ENST00000532699.1:n.314+32858C>T

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.314+32858C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,064 control chromosomes in the GnomAD database, including 13,261 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 0.38 (13261 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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
ENSG00000255292	ENST00000532699.1	n.314+32858C>T		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.319+32858C>T		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.314+32858C>T		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58344 AN: 151944 Hom.: 13241 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.384 AC: 58398 AN: 152064 Hom.: 13261 Cov.: 32 AF XY: 0.397 AC XY: 29507 AN XY: 74316

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.417

Alfa AF: 0.427 Hom.: 20089

Bravo AF: 0.375

Asia WGS AF: 0.674 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11214093; hg19: chr11-111992592;