chr11-121139091-C-T

Position:

• chr11-121139091-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005422.4(TECTA):​c.3543+1069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,134 control chromosomes in the GnomAD database, including 11,879 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 0.33 (11879 hom., cov: 32)
• Consequence: TECTA NM_005422.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

Genes affected

TECTA (HGNC:11720): (tectorin alpha) The tectorial membrane is an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. Alpha-tectorin is one of the major noncollagenous components of the tectorial membrane. Mutations in the TECTA gene have been shown to be responsible for autosomal dominant nonsyndromic hearing impairment and a recessive form of sensorineural pre-lingual non-syndromic deafness. [provided by RefSeq, Jul 2008]

TBCEL-TECTA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TECTA	NM_005422.4	c.3543+1069C>T		intron_variant		ENST00000392793.6	NP_005413.2
TBCEL-TECTA	NM_001378761.1	c.4500+1069C>T		intron_variant			NP_001365690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TECTA	ENST00000392793.6	c.3543+1069C>T		intron_variant		5	NM_005422.4	ENSP00000376543	P4
TECTA	ENST00000264037.2	c.3543+1069C>T		intron_variant		1		ENSP00000264037	P4
TECTA	ENST00000642222.1	c.3543+1069C>T		intron_variant				ENSP00000493855	A1
TECTA	ENST00000645008.1	c.850+1069C>T		intron_variant				ENSP00000496274

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49699 AN: 152016 Hom.: 11863 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.327 AC: 49754 AN: 152134 Hom.: 11879 Cov.: 32 AF XY: 0.318 AC XY: 23651 AN XY: 74380

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.302

Alfa AF: 0.267 Hom.: 2026

Bravo AF: 0.342

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.4
DANN	Benign	0.82

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: rs620778; hg19: chr11-121009800;