11-112173503-C-T

Variant names:

• chr11-112173503-C-T
• rs11214109
• ENST00000532699.1:n.*55+2829C>T

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.*55+2829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,608 control chromosomes in the GnomAD database, including 1,364 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 0.12 (1364 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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.*55+2829C>T		intron_variant	Intron 5 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.431+2973C>T		intron_variant	Intron 4 of 5	4
ENSG00000255292	ENST00000531744.5	n.*55+2829C>T		intron_variant	Intron 5 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18019 AN: 151490 Hom.: 1365 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.119 AC: 18040 AN: 151608 Hom.: 1364 Cov.: 32 AF XY: 0.122 AC XY: 9059 AN XY: 74026

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.0548

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0480 Hom.: 42

Bravo AF: 0.118

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.34

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: rs11214109; hg19: chr11-112044226;