rs7932890

Variant names:

• chr11-79357349-A-G
• rs7932890
• NM_001098816.3:c.-320-59806T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098816.3(TENM4):​c.-320-59806T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,232 control chromosomes in the GnomAD database, including 2,730 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 0.18 (2730 hom., cov: 33)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 10 publications found

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 Gene-Disease associations (from GenCC):

• tremor, hereditary essential, 5

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Laboratory for Molecular Medicine

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.-320-59806T>C		intron_variant	Intron 1 of 33	ENST00000278550.12	NP_001092286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM4	ENST00000278550.12	c.-320-59806T>C		intron_variant	Intron 1 of 33	5	NM_001098816.3	ENSP00000278550.7
TENM4	ENST00000528688.5	n.240-59806T>C		intron_variant	Intron 1 of 3	3
TENM4	ENST00000531583.1	n.441-59806T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27576 AN: 152114 Hom.: 2712 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.182 AC: 27637 AN: 152232 Hom.: 2730 Cov.: 33 AF XY: 0.179 AC XY: 13313 AN XY: 74430

African (AFR) AF: 0.259 AC: 10754 AN: 41510

American (AMR) AF: 0.120 AC: 1828 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3472

East Asian (EAS) AF: 0.0543 AC: 282 AN: 5194

South Asian (SAS) AF: 0.0768 AC: 371 AN: 4832

European-Finnish (FIN) AF: 0.178 AC: 1890 AN: 10604

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11568 AN: 68016

Other (OTH) AF: 0.164 AC: 347 AN: 2116

Alfa AF: 0.177 Hom.: 513

Bravo AF: 0.182

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.84
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7932890; hg19: chr11-79068394;