11-78847194-G-T

Position:

• chr11-78847194-G-T

Variant summary

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

The NM_001098816.3(TENM4):​c.1681+6910C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,196 control chromosomes in the GnomAD database, including 4,423 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 0.21 (4423 hom., cov: 33)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.1681+6910C>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.1681+6910C>A		intron_variant		5	NM_001098816.3	ENSP00000278550.7

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32141 AN: 152078 Hom.: 4424 Cov.: 33

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.211 AC: 32142 AN: 152196 Hom.: 4423 Cov.: 33 AF XY: 0.212 AC XY: 15796 AN XY: 74404

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.0520

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.252

Alfa AF: 0.276 Hom.: 8257

Bravo AF: 0.193

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.34

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: rs547292; hg19: chr11-78558239;