11-112121869-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.160 AC: 6625 AN: 41500

American (AMR) AF: 0.491 AC: 7508 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3464

East Asian (EAS) AF: 0.854 AC: 4406 AN: 5162

South Asian (SAS) AF: 0.610 AC: 2944 AN: 4824

European-Finnish (FIN) AF: 0.473 AC: 4990 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28894 AN: 67960

Other (OTH) AF: 0.417 AC: 879 AN: 2110

Alfa AF: 0.422 Hom.: 27350

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
PhyloP100		-0.78

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

Other links and lift over

dbSNP: rs11214093; hg19: chr11-111992592;