rs1371217

chr4-181594506-T-Achr4-181594506-T-G

Variant summary

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

The XM_017008385.2(TENM3):c.-399-144981T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,868 control chromosomes in the GnomAD database, including 18,195 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 0.49 (18195 hom., cov: 31)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-399-144981T>A		intron_variant
TENM3	XM_017008389.2	c.-399-144981T>A		intron_variant
TENM3	XM_017008390.2	c.-399-144981T>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73868 AN: 151750 Hom.: 18188 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.487 AC: 73890 AN: 151868 Hom.: 18195 Cov.: 31 AF XY: 0.484 AC XY: 35944 AN XY: 74192

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.456

Alfa AF: 0.344 Hom.: 886

Bravo AF: 0.487

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.1
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1371217; hg19: chr4-182515659;