4-182346995-C-CGG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001080477.4(TENM3):c.511+73_511+74dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 813,618 control chromosomes in the GnomAD database, including 17,074 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.25 (5688 hom., cov: 0)
  • Exomes 𝑓: 0.20 (11386 hom.)
• Consequence: TENM3 NM_001080477.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.190

Genes affected

TENM3 (HGNC:29944): (teneurin transmembrane protein 3) This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-182346995-C-CGG is Benign according to our data. Variant chr4-182346995-C-CGG is described in ClinVar as [Benign]. Clinvar id is 1282190.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	NM_001080477.4	c.511+73_511+74dup		intron_variant		ENST00000511685.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM3	ENST00000511685.6	c.511+73_511+74dup		intron_variant		5	NM_001080477.4	P1
TENM3	ENST00000513201.1	n.761+73_761+74dup		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37072 AN: 148502 Hom.: 5689 Cov.: 0

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.204 AC: 135404 AN: 665010 Hom.: 11386 AF XY: 0.204 AC XY: 67433 AN XY: 329886

Gnomad4 AFR exome AF: 0.0568

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.150

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.219

Gnomad4 FIN exome AF: 0.242

Gnomad4 NFE exome AF: 0.213

Gnomad4 OTH exome AF: 0.178

GnomAD4 genome AF: 0.249 AC: 37061 AN: 148608 Hom.: 5688 Cov.: 0 AF XY: 0.247 AC XY: 17829 AN XY: 72168

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.241

Alfa AF: 0.399 Hom.: 403

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 04, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11373586; hg19: chr4-183268148;