rs7931512

Variant names:

• chr11-79309244-A-G
• rs7931512
• NM_001098816.3:c.-320-11701T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-79309244-A-G
• chr11-79309244-A-T

Variant summary

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

The NM_001098816.3(TENM4):​c.-320-11701T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,216 control chromosomes in the GnomAD database, including 4,627 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 0.24 (4627 hom., cov: 33)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.-320-11701T>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.-320-11701T>C		intron_variant	Intron 1 of 33	5	NM_001098816.3	ENSP00000278550.7
TENM4	ENST00000528688.5	n.240-11701T>C		intron_variant	Intron 1 of 3	3
TENM4	ENST00000531583.1	n.441-11701T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36261 AN: 152098 Hom.: 4624 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.238 AC: 36288 AN: 152216 Hom.: 4627 Cov.: 33 AF XY: 0.233 AC XY: 17307 AN XY: 74418

African (AFR) AF: 0.291 AC: 12074 AN: 41494

American (AMR) AF: 0.161 AC: 2461 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.177 AC: 853 AN: 4830

European-Finnish (FIN) AF: 0.213 AC: 2257 AN: 10608

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16726 AN: 68000

Other (OTH) AF: 0.230 AC: 486 AN: 2112

Alfa AF: 0.237 Hom.: 8746

Bravo AF: 0.236

Asia WGS AF: 0.119 AC: 413 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	1.7
DANN	Benign	0.68
PhyloP100		-0.10
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: rs7931512; hg19: chr11-79020289;