11-112121869-C-T

Position:

• chr11-112121869-C-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/exons	MANE	Protein	UniProt
		n.112121869C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255292	ENST00000532699.1	n.314+32858C>T		intron_variant		3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.319+32858C>T		intron_variant		4
ENSG00000255292	ENST00000531744.5	n.314+32858C>T		intron_variant		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;