rs1450140

Positions:

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

Variant summary

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

The NR_125905.1(TENM3-AS1):​n.2173G>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_125905.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

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

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3-AS1	NR_125905.1	n.2173G>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM3-AS1	ENST00000509012.5	n.149+4214G>T		intron_variant, non_coding_transcript_variant		4
TENM3-AS1	ENST00000507869.6	n.112+4214G>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.420

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1450140; hg19: chr4-183060986;