11-79123080-A-T

Position:

• chr11-79123080-A-T

Variant summary

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

The NM_001098816.3(TENM4):​c.-66+25630T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,888 control chromosomes in the GnomAD database, including 14,663 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 0.44 (14663 hom., cov: 31)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

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]

TENM4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.-66+25630T>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.-66+25630T>A		intron_variant		5	NM_001098816.3	ENSP00000278550.7
TENM4	ENST00000532654.5	n.287+25630T>A		intron_variant		1
TENM4	ENST00000527736.5	c.-65-53071T>A		intron_variant		5		ENSP00000433535.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66030 AN: 151770 Hom.: 14631 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.435 AC: 66122 AN: 151888 Hom.: 14663 Cov.: 31 AF XY: 0.434 AC XY: 32174 AN XY: 74210

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.464

Alfa AF: 0.446 Hom.: 1834

Bravo AF: 0.430

Asia WGS AF: 0.448 AC: 1559 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.2
DANN	Benign	0.82

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: rs948763; hg19: chr11-78834125;