rs6815990

Positions:

• chr4-182174165-C-T

Variant summary

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

The ENST00000505389.1(ENSG00000248266):​n.121-16052C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,720 control chromosomes in the GnomAD database, including 27,847 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 0.60 (27847 hom., cov: 31)
• Consequence: ENST00000505389.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

(HGNC:):

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	NM_001415966.1	c.-76+29411C>T		intron_variant
TENM3	NM_001415967.1	c.-76+29411C>T		intron_variant
TENM3	NM_001415968.1	c.-76+29411C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000505389.1	n.121-16052C>T		intron_variant, non_coding_transcript_variant		3
TENM3	ENST00000513201.1	n.175+30004C>T		intron_variant, non_coding_transcript_variant		1
TENM3	ENST00000512480.5	c.-76+29411C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91047 AN: 151602 Hom.: 27829 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.552

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.600 AC: 91096 AN: 151720 Hom.: 27847 Cov.: 31 AF XY: 0.597 AC XY: 44225 AN XY: 74134

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.572

Alfa AF: 0.646 Hom.: 3948

Bravo AF: 0.579

Asia WGS AF: 0.492 AC: 1701 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6815990; hg19: chr4-183095318;