chr11-112139169-C-T

Variant names:

• chr11-112139169-C-T
• rs10891329
• ENST00000532699.1:n.315-31250C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532699.1(ENSG00000255292):​n.315-31250C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,896 control chromosomes in the GnomAD database, including 10,929 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 0.37 (10929 hom., cov: 31)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 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.315-31250C>T		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.320-31250C>T		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.315-31250C>T		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56725 AN: 151778 Hom.: 10904 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.374 AC: 56791 AN: 151896 Hom.: 10929 Cov.: 31 AF XY: 0.376 AC XY: 27899 AN XY: 74254

African (AFR) AF: 0.437 AC: 18068 AN: 41374

American (AMR) AF: 0.376 AC: 5741 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5168

South Asian (SAS) AF: 0.586 AC: 2814 AN: 4806

European-Finnish (FIN) AF: 0.272 AC: 2866 AN: 10536

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22404 AN: 67976

Other (OTH) AF: 0.401 AC: 845 AN: 2106

Alfa AF: 0.353 Hom.: 1551

Bravo AF: 0.377

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.46
PhyloP100		0.045

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: rs10891329; hg19: chr11-112009892;