rs17071568

chr4-181476379-G-Achr4-181476379-G-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+28607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,770 control chromosomes in the GnomAD database, including 10,357 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 0.36 (10357 hom., cov: 31)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-400+28607G>A		intron_variant
TENM3	XM_017008389.2	c.-400+28607G>A		intron_variant
TENM3	XM_017008390.2	c.-400+28607G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54809 AN: 151650 Hom.: 10337 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.362 AC: 54870 AN: 151770 Hom.: 10357 Cov.: 31 AF XY: 0.360 AC XY: 26704 AN XY: 74156

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.352

Alfa AF: 0.307 Hom.: 2974

Bravo AF: 0.374

Asia WGS AF: 0.328 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.079
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17071568; hg19: chr4-182397532;