chr10-112284525-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_058222.3(TECTB):​c.77-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,594,504 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 3 hom. )

Consequence

TECTB
NM_058222.3 intron

Scores

2
Splicing: ADA: 0.000008836
2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.458
Variant links:
Genes affected
TECTB (HGNC:11721): (tectorin beta) This gene encodes a non-collagenous glycoprotein component of the tectorial membrane, which covers the auditory hair cells in the cochlea of the inner ear. A similar protein in mouse functions in low-frequency hearing. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 10-112284525-C-T is Benign according to our data. Variant chr10-112284525-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3053331.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TECTBNM_058222.3 linkc.77-10C>T intron_variant Intron 2 of 10 ENST00000646139.2 NP_478129.1 Q96PL2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TECTBENST00000646139.2 linkc.77-10C>T intron_variant Intron 2 of 10 NM_058222.3 ENSP00000494896.1 Q96PL2
TECTBENST00000369422.4 linkc.77-10C>T intron_variant Intron 1 of 9 1 ENSP00000358430.3 Q96PL2
TECTBENST00000643850.1 linkc.77-10C>T intron_variant Intron 2 of 10 ENSP00000495832.1 A0A2R8YGB5
TECTBENST00000645243.1 linkc.77-10C>T intron_variant Intron 2 of 10 ENSP00000495514.1 A0A2R8Y6R9

Frequencies

GnomAD3 genomes
AF:
0.00277
AC:
421
AN:
152176
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00898
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00255
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000862
AC:
207
AN:
240098
Hom.:
0
AF XY:
0.000680
AC XY:
88
AN XY:
129344
show subpopulations
Gnomad AFR exome
AF:
0.00935
Gnomad AMR exome
AF:
0.000948
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000183
Gnomad OTH exome
AF:
0.00103
GnomAD4 exome
AF:
0.000331
AC:
477
AN:
1442210
Hom.:
3
Cov.:
30
AF XY:
0.000299
AC XY:
214
AN XY:
715092
show subpopulations
Gnomad4 AFR exome
AF:
0.00867
Gnomad4 AMR exome
AF:
0.00125
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:
0.0000927
Gnomad4 OTH exome
AF:
0.000520
GnomAD4 genome
AF:
0.00276
AC:
421
AN:
152294
Hom.:
1
Cov.:
33
AF XY:
0.00286
AC XY:
213
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.00895
Gnomad4 AMR
AF:
0.00255
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00189
Hom.:
0
Bravo
AF:
0.00309

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

TECTB-related disorder Benign:1
Apr 01, 2019
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
CADD
Benign
0.63
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0000088
dbscSNV1_RF
Benign
0.038
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs143737351; hg19: chr10-114044283; API