chr10-112287637-T-C

Variant names:

• chr10-112287637-T-C
• rs943265
• NM_058222.3:c.483+1246T>C

Variant summary

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

The NM_058222.3(TECTB):​c.483+1246T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,094 control chromosomes in the GnomAD database, including 2,445 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 (2445 hom., cov: 32)
• Consequence: TECTB NM_058222.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 3 publications found

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]

ENSG00000288938 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TECTB	NM_058222.3	c.483+1246T>C		intron_variant	Intron 5 of 10	ENST00000646139.2	NP_478129.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TECTB	ENST00000646139.2	c.483+1246T>C		intron_variant	Intron 5 of 10		NM_058222.3	ENSP00000494896.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25254 AN: 151976 Hom.: 2439 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.166 AC: 25286 AN: 152094 Hom.: 2445 Cov.: 32 AF XY: 0.170 AC XY: 12611 AN XY: 74348

African (AFR) AF: 0.0978 AC: 4058 AN: 41514

American (AMR) AF: 0.263 AC: 4023 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1762 AN: 5154

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4824

European-Finnish (FIN) AF: 0.152 AC: 1610 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11691 AN: 67954

Other (OTH) AF: 0.172 AC: 363 AN: 2110

Alfa AF: 0.170 Hom.: 1840

Bravo AF: 0.170

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		0.068
Mutation Taster		=100/0	polymorphism (auto)

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: rs943265; hg19: chr10-114047395;