rs33933747

Variant names:

• chr4-182346575-TAAA-T
• rs33933747
• NM_001080477.4:c.233-64_233-62delAAA

Your query was ambiguous. Multiple possible variants found:

• chr4-182346575-TAAA-T
• chr4-182346575-TAAA-TA
• chr4-182346575-TAAA-TAA
• chr4-182346575-TAAA-TAAAA
• chr4-182346575-TAAA-TAAAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_001080477.4(TENM3):​c.233-64_233-62delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00089 in 875,696 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000034 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0011 (0 hom.)
• Consequence: TENM3 NM_001080477.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00106 (774/729296) while in subpopulation AMR AF= 0.00116 (19/16392). AF 95% confidence interval is 0.00108. There are 0 homozygotes in gnomad4_exome. There are 424 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM3	NM_001080477.4	c.233-64_233-62delAAA		intron_variant	Intron 2 of 27	ENST00000511685.6	NP_001073946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM3	ENST00000511685.6	c.233-75_233-73delAAA		intron_variant	Intron 2 of 27	5	NM_001080477.4	ENSP00000424226.1
TENM3	ENST00000513201.1	n.483-75_483-73delAAA		intron_variant	Intron 2 of 3	1
TENM3	ENST00000512480.5	c.233-75_233-73delAAA		intron_variant	Intron 2 of 2	3		ENSP00000421320.1

Frequencies

GnomAD3 genomes AF: 0.0000342 AC: 5 AN: 146400 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000292

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000337

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000150

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00106 AC: 774 AN: 729296 Hom.: 0 AF XY: 0.00116 AC XY: 424 AN XY: 364532

Gnomad4 AFR exome AF: 0.000824

Gnomad4 AMR exome AF: 0.00116

Gnomad4 ASJ exome AF: 0.000510

Gnomad4 EAS exome AF: 0.000376

Gnomad4 SAS exome AF: 0.00115

Gnomad4 FIN exome AF: 0.000583

Gnomad4 NFE exome AF: 0.00116

Gnomad4 OTH exome AF: 0.000671

GnomAD4 genome AF: 0.0000342 AC: 5 AN: 146400 Hom.: 0 Cov.: 0 AF XY: 0.0000422 AC XY: 3 AN XY: 71020

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000292

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000337

Gnomad4 NFE AF: 0.0000150

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs33933747; hg19: chr4-183267728;