Variant 19-43418335-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The ENST00000598265.2(TEX101):c.688C>T(p.Pro230Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

TEX101
ENST00000598265.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0210

Variant links:

Genes affected

TEX101 (HGNC:30722): (testis expressed 101) Predicted to be involved in binding activity of sperm to zona pellucida; flagellated sperm motility; and regulation of flagellated sperm motility. Predicted to be located in acrosomal vesicle; extracellular region; and plasma membrane. Predicted to be active in plasma membrane raft. Predicted to be anchored component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TEX101 links:

TEX101 (HGNC:):

TEX101 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.061788946).

BP6

Variant 19-43418335-C-T is Benign according to our data. Variant chr19-43418335-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2272754.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX101	NM_001130011.3 linkuse as main transcript	c.688C>T	p.Pro230Ser	missense_variant	6/6	ENST00000598265.2	NP_001123483.1	Q9BY14-1
TEX101	NM_031451.5 linkuse as main transcript	c.742C>T	p.Pro248Ser	missense_variant	9/9		NP_113639.4	Q9BY14-2A0A024R0T7
TEX101	XM_005259303.4 linkuse as main transcript	c.784C>T	p.Pro262Ser	missense_variant	6/6		XP_005259360.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TEX101	ENST00000598265.2 linkuse as main transcript	c.688C>T	p.Pro230Ser	missense_variant	6/6	1	NM_001130011.3	ENSP00000472769.1	Q9BY14-1
TEX101	ENST00000602198.5 linkuse as main transcript	c.742C>T	p.Pro248Ser	missense_variant	8/8	5		ENSP00000472308.1	Q9BY14-2
TEX101	ENST00000601707.1 linkuse as main transcript	n.792C>T		non_coding_transcript_exon_variant	6/6	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461884

Hom.:

Cov.:

AF XY:

0.00000275

AC XY:

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 26, 2022

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.60

DANN

Benign

0.15

DEOGEN2

Benign

0.00082

.;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.00089

LIST_S2

Benign

0.44

T;T

M_CAP

Benign

0.0012

MetaRNN

Benign

0.062

T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

-0.050

.;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.23

Sift4G

Benign

1.0

T;T

Polyphen

0.0090

B;B

Vest4

0.14

MutPred

0.50

.;Gain of catalytic residue at P230 (P = 0.0169);

MVP

0.081

MPC

0.090

ClinPred

0.036

GERP RS

0.037

Varity_R

0.025

gMVP

0.43

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over