rs597444

Variant names:

• chr11-79272928-T-A
• rs597444
• NM_001098816.3:c.-265+24560A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-79272928-T-A
• chr11-79272928-T-C
• chr11-79272928-T-G

Variant summary

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

The NM_001098816.3(TENM4):​c.-265+24560A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,964 control chromosomes in the GnomAD database, including 25,048 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 0.56 (25048 hom., cov: 32)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.-265+24560A>T		intron_variant	Intron 2 of 33	ENST00000278550.12	NP_001092286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM4	ENST00000278550.12	c.-265+24560A>T		intron_variant	Intron 2 of 33	5	NM_001098816.3	ENSP00000278550.7
TENM4	ENST00000528688.5	n.295+24560A>T		intron_variant	Intron 2 of 3	3
TENM4	ENST00000531583.1	n.496+24560A>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85446 AN: 151846 Hom.: 25041 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.562 AC: 85478 AN: 151964 Hom.: 25048 Cov.: 32 AF XY: 0.557 AC XY: 41388 AN XY: 74286

African (AFR) AF: 0.417 AC: 17283 AN: 41434

American (AMR) AF: 0.645 AC: 9850 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1780 AN: 3466

East Asian (EAS) AF: 0.304 AC: 1572 AN: 5164

South Asian (SAS) AF: 0.482 AC: 2315 AN: 4806

European-Finnish (FIN) AF: 0.569 AC: 6001 AN: 10548

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.660 AC: 44834 AN: 67946

Other (OTH) AF: 0.561 AC: 1187 AN: 2116

Alfa AF: 0.513 Hom.: 1595

Bravo AF: 0.564

Asia WGS AF: 0.416 AC: 1448 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	0.24
DANN	Benign	0.82
PhyloP100		-0.81
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: rs597444; hg19: chr11-78983973;