11-79066002-C-T

Position:

• chr11-79066002-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.224-995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,210 control chromosomes in the GnomAD database, including 62,614 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 0.90 (62614 hom., cov: 33)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.224-995G>A		intron_variant		ENST00000278550.12	NP_001092286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM4	ENST00000278550.12	c.224-995G>A		intron_variant		5	NM_001098816.3	ENSP00000278550	P1
TENM4	ENST00000532654.5	n.576-995G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137524 AN: 152090 Hom.: 62579 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.904 AC: 137613 AN: 152210 Hom.: 62614 Cov.: 33 AF XY: 0.901 AC XY: 67038 AN XY: 74406

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.909

Alfa AF: 0.928 Hom.: 27600

Bravo AF: 0.893

Asia WGS AF: 0.712 AC: 2478 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	0.012
DANN	Benign	0.63

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: rs7937442; hg19: chr11-78777047;