14-105411381-C-T

Variant names:

• chr14-105411381-C-T
• NM_001195082.2:c.164C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001195082.2(TEX22):​c.164C>T​(p.Pro55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEX22 NM_001195082.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.06
• Publications: 0 publications found

Genes affected

TEX22 (HGNC:40026): (testis expressed 22) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13497183).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195082.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX22	NM_001195082.2	MANE Select	c.164C>T	p.Pro55Leu	missense	Exon 3 of 4	NP_001182011.1	C9J3V5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX22	ENST00000451127.3	TSL:2 MANE Select	c.164C>T	p.Pro55Leu	missense	Exon 3 of 4	ENSP00000397002.2	C9J3V5
	TEX22	ENST00000906980.1		c.164C>T	p.Pro55Leu	missense	Exon 3 of 4	ENSP00000577039.1
	TEX22	ENST00000935983.1		c.164C>T	p.Pro55Leu	missense	Exon 2 of 3	ENSP00000606042.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1173516 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 571922

African (AFR) AF: 0.00 AC: 0 AN: 23502

American (AMR) AF: 0.00 AC: 0 AN: 14122

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17328

East Asian (EAS) AF: 0.00 AC: 0 AN: 25920

South Asian (SAS) AF: 0.00 AC: 0 AN: 46880

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26306

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3176

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 969640

Other (OTH) AF: 0.00 AC: 0 AN: 46642

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.95
DEOGEN2	Benign	0.081	T
Eigen	Benign	-0.95
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.034	N
LIST_S2	Benign	0.54	T
M_CAP	Uncertain	0.27	D
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.55	N
PhyloP100		-1.1
PrimateAI	Uncertain	0.61	T
PROVEAN	Pathogenic	-5.9	D
REVEL	Benign	0.036
Sift	Benign	0.16	T
Sift4G	Benign	0.29	T
Polyphen		0.71	P
Vest4		0.18
MutPred		0.22		Loss of glycosylation at P55 (P = 0.0048)
MVP		0.28
ClinPred		0.84	D
GERP RS		-1.6
Varity_R		0.067
gMVP		0.015
Mutation Taster		=100/0	polymorphism

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

hg19: chr14-105877718;