4-182346631-C-CT

Position:

• chr4-182346631-C-CT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS1

The NM_001080477.4(TENM3):​c.233-13dup variant causes a intron change. The variant allele was found at a frequency of 0.000437 in 1,603,410 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0023 (1 hom., cov: 31)
  • Exomes 𝑓: 0.00024 (1 hom.)
• Consequence: TENM3 NM_001080477.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.93

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 4-182346631-C-CT is Benign according to our data. Variant chr4-182346631-C-CT is described in ClinVar as [Benign]. Clinvar id is 1899079.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00228 (346/151464) while in subpopulation AFR AF= 0.00803 (332/41340). AF 95% confidence interval is 0.00732. There are 1 homozygotes in gnomad4. There are 157 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	NM_001080477.4	c.233-13dup		intron_variant		ENST00000511685.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM3	ENST00000511685.6	c.233-13dup		intron_variant		5	NM_001080477.4	P1
TENM3	ENST00000513201.1	n.483-13dup		intron_variant, non_coding_transcript_variant		1
TENM3	ENST00000512480.5	c.233-13dup		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00229 AC: 347 AN: 151368 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00808

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000657

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000295

Gnomad OTH AF: 0.000962

GnomAD3 exomes AF: 0.000570 AC: 138 AN: 242210 Hom.: 0 AF XY: 0.000403 AC XY: 53 AN XY: 131390

Gnomad AFR exome AF: 0.00836

Gnomad AMR exome AF: 0.000298

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000244 AC: 355 AN: 1451946 Hom.: 1 Cov.: 32 AF XY: 0.000183 AC XY: 132 AN XY: 722422

Gnomad4 AFR exome AF: 0.00931

Gnomad4 AMR exome AF: 0.000226

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000234

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000543

Gnomad4 OTH exome AF: 0.000450

GnomAD4 genome AF: 0.00228 AC: 346 AN: 151464 Hom.: 1 Cov.: 31 AF XY: 0.00212 AC XY: 157 AN XY: 74004

Gnomad4 AFR AF: 0.00803

Gnomad4 AMR AF: 0.000657

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000295

Gnomad4 OTH AF: 0.000952

Bravo AF: 0.00257

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

Invitae

Feb 14, 2022

- -

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: rs571729819; hg19: chr4-183267784;