rs10891323

Variant names:

• chr11-112122402-T-C
• rs10891323
• ENST00000532699.1:n.314+33391T>C

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.314+33391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 152,226 control chromosomes in the GnomAD database, including 618 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 0.078 (618 hom., cov: 32)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

ENSG00000255292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 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+33391T>C		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.319+33391T>C		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.314+33391T>C		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11913 AN: 152108 Hom.: 618 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0782 AC: 11910 AN: 152226 Hom.: 618 Cov.: 32 AF XY: 0.0760 AC XY: 5659 AN XY: 74444

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0551

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.103 Hom.: 471

Bravo AF: 0.0743

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.93
DANN	Benign	0.72

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: rs10891323; hg19: chr11-111993125;