rs7904701

chr10-112287050-T-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TECTB	NM_058222.3	c.483+659T>A		intron_variant		ENST00000646139.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TECTB	ENST00000646139.2	c.483+659T>A		intron_variant			NM_058222.3	P1
TECTB	ENST00000369422.4	c.483+659T>A		intron_variant		1		P1
TECTB	ENST00000643850.1	c.513+659T>A		intron_variant
TECTB	ENST00000645243.1	c.483+659T>A		intron_variant

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.416

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

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

LitVar

Other links and lift over

dbSNP: rs7904701; hg19: chr10-114046808;