chr11-112166291-G-T

Variant names:

• chr11-112166291-G-T
• rs5744222
• ENST00000532699.1:n.315-4128G>T

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-4128G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,110 control chromosomes in the GnomAD database, including 2,857 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 0.17 (2857 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824
• Publications: 19 publications found

Genes affected

ENSG00000255292 (HGNC:):

ENSG00000254638 (HGNC:58436):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX12-AS1	XR_001748384.2	n.82-115C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255292	ENST00000532699.1	n.315-4128G>T		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.320-4128G>T		intron_variant	Intron 3 of 5	4
ENSG00000254638	ENST00000527589.1	n.171-115C>A		intron_variant	Intron 2 of 3	3
ENSG00000255292	ENST00000531744.5	n.315-4128G>T		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25385 AN: 151994 Hom.: 2856 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.167 AC: 25383 AN: 152110 Hom.: 2857 Cov.: 32 AF XY: 0.163 AC XY: 12120 AN XY: 74342

African (AFR) AF: 0.0462 AC: 1920 AN: 41552

American (AMR) AF: 0.143 AC: 2178 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.00522 AC: 27 AN: 5174

South Asian (SAS) AF: 0.0828 AC: 399 AN: 4820

European-Finnish (FIN) AF: 0.249 AC: 2628 AN: 10542

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17098 AN: 67952

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.224 Hom.: 2224

Bravo AF: 0.156

Asia WGS AF: 0.0390 AC: 136 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.35
DANN	Benign	0.39
PhyloP100		-0.82

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: rs5744222; hg19: chr11-112037014;