rs11214108

Variant names:

• chr11-112172891-G-A
• rs11214108
• ENST00000532699.1:n.*55+2217G>A

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.*55+2217G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,056 control chromosomes in the GnomAD database, including 1,355 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 (1355 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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+2217G>A		intron_variant	Intron 5 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.431+2361G>A		intron_variant	Intron 4 of 5	4
ENSG00000255292	ENST00000531744.5	n.*55+2217G>A		intron_variant	Intron 5 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17888 AN: 151938 Hom.: 1356 Cov.: 32

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.0545

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: 0.118 AC: 17907 AN: 152056 Hom.: 1355 Cov.: 32 AF XY: 0.121 AC XY: 9010 AN XY: 74308

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.132

Alfa AF: 0.119 Hom.: 1445

Bravo AF: 0.117

Asia WGS AF: 0.177 AC: 613 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.28

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: rs11214108; hg19: chr11-112043614;