chr10-112287050-T-A

Variant names:

• chr10-112287050-T-A
• rs7904701
• NM_058222.3:c.483+659T>A

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+659T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,120 control chromosomes in the GnomAD database, including 13,819 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 0.41 (13819 hom., cov: 33)
• Consequence: TECTB NM_058222.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TECTB	NM_058222.3	c.483+659T>A		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+659T>A		intron_variant	Intron 5 of 10		NM_058222.3	ENSP00000494896.1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63029 AN: 152002 Hom.: 13790 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.415 AC: 63100 AN: 152120 Hom.: 13819 Cov.: 33 AF XY: 0.421 AC XY: 31275 AN XY: 74368

African (AFR) AF: 0.487 AC: 20204 AN: 41470

American (AMR) AF: 0.529 AC: 8085 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1272 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3184 AN: 5174

South Asian (SAS) AF: 0.503 AC: 2425 AN: 4822

European-Finnish (FIN) AF: 0.329 AC: 3475 AN: 10578

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23288 AN: 67994

Other (OTH) AF: 0.416 AC: 878 AN: 2110

Alfa AF: 0.387 Hom.: 1478

Bravo AF: 0.433

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.76
DANN	Benign	0.62
PhyloP100		-0.54
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: rs7904701; hg19: chr10-114046808;