rs501435

chr11-79162576-C-T

Variant summary

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

The NM_001098816.3(TENM4):c.-162-13770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,998 control chromosomes in the GnomAD database, including 43,573 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 0.75 (43573 hom., cov: 31)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

Genes affected

TENM4 (HGNC:29945): (teneurin transmembrane protein 4) The protein encoded by this gene plays a role in establishing proper neuronal connectivity during development. Defects in this gene have been associated with hereditary essential tremor-5. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM4	NM_001098816.3	c.-162-13770G>A		intron_variant		ENST00000278550.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM4	ENST00000278550.12	c.-162-13770G>A		intron_variant		5	NM_001098816.3	P1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113391 AN: 151882 Hom.: 43552 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.746 AC: 113450 AN: 151998 Hom.: 43573 Cov.: 31 AF XY: 0.738 AC XY: 54826 AN XY: 74288

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.759

Alfa AF: 0.832 Hom.: 73196

Bravo AF: 0.730

Asia WGS AF: 0.566 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.32
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs501435; hg19: chr11-78873621;