rs1450140

Variant names:

• chr4-182139833-C-A
• rs1450140
• XM_017008385.2:c.-76+98090C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-182139833-C-A
• chr4-182139833-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027107.2(TENM3-AS1):​n.4126G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,070 control chromosomes in the GnomAD database, including 13,603 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 0.42 (13603 hom., cov: 34)
• Consequence: TENM3-AS1 NR_027107.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 9 publications found

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]

TENM3-AS1 (HGNC:28076): (TENM3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_027107.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM3-AS1	NR_027107.2		n.4126G>T		non_coding_transcript_exon	Exon 4 of 4
	TENM3-AS1	NR_125905.1		n.2173G>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENM3-AS1	ENST00000505537.2	TSL:3	n.196+4214G>T		intron	N/A
	TENM3-AS1	ENST00000507869.7	TSL:2	n.129+4214G>T		intron	N/A
	TENM3-AS1	ENST00000509012.5	TSL:4	n.149+4214G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63720 AN: 151952 Hom.: 13601 Cov.: 34

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.419 AC: 63743 AN: 152070 Hom.: 13603 Cov.: 34 AF XY: 0.416 AC XY: 30950 AN XY: 74332

African (AFR) AF: 0.403 AC: 16725 AN: 41490

American (AMR) AF: 0.312 AC: 4769 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1795 AN: 5144

South Asian (SAS) AF: 0.393 AC: 1890 AN: 4814

European-Finnish (FIN) AF: 0.414 AC: 4378 AN: 10566

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30960 AN: 67980

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.342 Hom.: 1413

Bravo AF: 0.411

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.039
DANN	Benign	0.71
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1450140; hg19: chr4-183060986;