rs6815916

Positions:

• chr4-181631890-A-G

Variant summary

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

The XM_017008385.2(TENM3):​c.-399-107597A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,162 control chromosomes in the GnomAD database, including 641 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 0.089 (641 hom., cov: 32)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3	XM_017008385.2	c.-399-107597A>G		intron_variant			XP_016863874.1
TENM3	XM_017008389.2	c.-399-107597A>G		intron_variant			XP_016863878.1
TENM3	XM_017008390.2	c.-399-107597A>G		intron_variant			XP_016863879.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13567 AN: 152044 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0892 AC: 13579 AN: 152162 Hom.: 641 Cov.: 32 AF XY: 0.0900 AC XY: 6696 AN XY: 74382

Gnomad4 AFR AF: 0.0998

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0884 Hom.: 853

Bravo AF: 0.0873

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6815916; hg19: chr4-182553043;