4-182346575-TA-T

Variant summary

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

The NM_001080477.4(TENM3):c.233-62del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.90 (59674 hom., cov: 0)
  • Exomes 𝑓: 0.56 (44410 hom.)
  • Failed GnomAD Quality Control
• Consequence: TENM3 NM_001080477.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.48

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 4-182346575-TA-T is Benign according to our data. Variant chr4-182346575-TA-T is described in ClinVar as [Benign]. Clinvar id is 1256668.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	NM_001080477.4	c.233-62del		intron_variant		ENST00000511685.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM3	ENST00000511685.6	c.233-62del		intron_variant		5	NM_001080477.4	P1
TENM3	ENST00000513201.1	n.483-62del		intron_variant, non_coding_transcript_variant		1
TENM3	ENST00000512480.5	c.233-62del		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.901 AC: 131984 AN: 146410 Hom.: 59668 Cov.: 0

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.900

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.556 AC: 407250 AN: 732270 Hom.: 44410 AF XY: 0.554 AC XY: 202902 AN XY: 366066

Gnomad4 AFR exome AF: 0.515

Gnomad4 AMR exome AF: 0.528

Gnomad4 ASJ exome AF: 0.522

Gnomad4 EAS exome AF: 0.543

Gnomad4 SAS exome AF: 0.529

Gnomad4 FIN exome AF: 0.571

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.548

GnomAD4 genome AF: 0.901 AC: 132015 AN: 146470 Hom.: 59674 Cov.: 0 AF XY: 0.902 AC XY: 64129 AN XY: 71106

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.900

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

May 17, 2021

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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: rs33933747; hg19: chr4-183267728;