4-181631890-A-G

Position:

• chr4-181631890-A-G

Variant summary

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

The XM_017008385.2(TENM3):​c.-399-107597A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,162 control chromosomes in the GnomAD database, including 641 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 0.089 (641 hom., cov: 32)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-399-107597A>G		intron_variant
TENM3	XM_017008389.2	c.-399-107597A>G		intron_variant
TENM3	XM_017008390.2	c.-399-107597A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13567 AN: 152044 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0892 AC: 13579 AN: 152162 Hom.: 641 Cov.: 32 AF XY: 0.0900 AC XY: 6696 AN XY: 74382

Gnomad4 AFR AF: 0.0998

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0884 Hom.: 853

Bravo AF: 0.0873

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6815916; hg19: chr4-182553043;