4-182346995-C-CG

Variant summary

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

The NM_001080477.4(TENM3):c.511+74dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 843,882 control chromosomes in the GnomAD database, including 242,071 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.73 (40681 hom., cov: 0)
  • Exomes 𝑓: 0.77 (201390 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-CG is Benign according to our data. Variant chr4-182346995-C-CG is described in ClinVar as [Benign]. Clinvar id is 1229849.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.731 AC: 109175 AN: 149310 Hom.: 40642 Cov.: 0

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.742

GnomAD4 exome AF: 0.772 AC: 535919 AN: 694466 Hom.: 201390 AF XY: 0.771 AC XY: 265957 AN XY: 345014

Gnomad4 AFR exome AF: 0.858

Gnomad4 AMR exome AF: 0.854

Gnomad4 ASJ exome AF: 0.801

Gnomad4 EAS exome AF: 0.811

Gnomad4 SAS exome AF: 0.755

Gnomad4 FIN exome AF: 0.732

Gnomad4 NFE exome AF: 0.767

Gnomad4 OTH exome AF: 0.789

GnomAD4 genome AF: 0.731 AC: 109259 AN: 149416 Hom.: 40681 Cov.: 0 AF XY: 0.733 AC XY: 53242 AN XY: 72672

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.740

Alfa AF: 0.596 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

- -

Computational scores

Source: dbNSFP v4.3

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: rs11373586; hg19: chr4-183268148;