11-79387057-C-G

Variant summary

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

The NM_001098816.3(TENM4):c.-321+53452G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,992 control chromosomes in the GnomAD database, including 7,754 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 0.32 (7754 hom., cov: 32)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM4	NM_001098816.3	c.-321+53452G>C		intron_variant		ENST00000278550.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM4	ENST00000278550.12	c.-321+53452G>C		intron_variant		5	NM_001098816.3	P1
TENM4	ENST00000528688.5	n.239+51905G>C		intron_variant, non_coding_transcript_variant		3
TENM4	ENST00000531583.1	n.440+53452G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48801 AN: 151874 Hom.: 7746 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.321 AC: 48843 AN: 151992 Hom.: 7754 Cov.: 32 AF XY: 0.321 AC XY: 23824 AN XY: 74290

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.307

Alfa AF: 0.190 Hom.: 386

Bravo AF: 0.319

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.4
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs514536; hg19: chr11-79098101;