rs7672826

Positions:

• chr4-181478542-G-A

Variant summary

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

The XM_017008385.2(TENM3):​c.-400+30770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,918 control chromosomes in the GnomAD database, including 10,696 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 0.37 (10696 hom., cov: 32)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3	XM_017008385.2	c.-400+30770G>A		intron_variant			XP_016863874.1
TENM3	XM_017008389.2	c.-400+30770G>A		intron_variant			XP_016863878.1
TENM3	XM_017008390.2	c.-400+30770G>A		intron_variant			XP_016863879.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55679 AN: 151800 Hom.: 10671 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.367 AC: 55750 AN: 151918 Hom.: 10696 Cov.: 32 AF XY: 0.366 AC XY: 27202 AN XY: 74248

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.357

Alfa AF: 0.331 Hom.: 13824

Bravo AF: 0.380

Asia WGS AF: 0.343 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7672826; hg19: chr4-182399695;