rs1439283

Positions:

• chr4-181563616-C-T

Variant summary

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

The XM_017008385.2(TENM3):​c.-400+115844C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,018 control chromosomes in the GnomAD database, including 18,125 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 0.48 (18125 hom., cov: 32)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3	XM_017008385.2	c.-400+115844C>T		intron_variant			XP_016863874.1
TENM3	XM_017008389.2	c.-400+115844C>T		intron_variant			XP_016863878.1
TENM3	XM_017008390.2	c.-400+115844C>T		intron_variant			XP_016863879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72401 AN: 151900 Hom.: 18096 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.477 AC: 72489 AN: 152018 Hom.: 18125 Cov.: 32 AF XY: 0.467 AC XY: 34670 AN XY: 74298

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.466

Alfa AF: 0.466 Hom.: 22580

Bravo AF: 0.498

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439283; hg19: chr4-182484769;