rs1439283

Positions:

• chr4-181563616-C-T

Variant summary

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

The XM_017008385.2(TENM3):​c.-400+115844C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,018 control chromosomes in the GnomAD database, including 18,125 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 0.48 (18125 hom., cov: 32)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-400+115844C>T		intron_variant
TENM3	XM_017008389.2	c.-400+115844C>T		intron_variant
TENM3	XM_017008390.2	c.-400+115844C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72401 AN: 151900 Hom.: 18096 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.477 AC: 72489 AN: 152018 Hom.: 18125 Cov.: 32 AF XY: 0.467 AC XY: 34670 AN XY: 74298

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.466

Alfa AF: 0.466 Hom.: 22580

Bravo AF: 0.498

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439283; hg19: chr4-182484769;