rs11826937

chr11-78948100-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.494-44577T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 152,196 control chromosomes in the GnomAD database, including 1,073 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 0.090 (1073 hom., cov: 33)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM4	NM_001098816.3	c.494-44577T>A		intron_variant		ENST00000278550.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM4	ENST00000278550.12	c.494-44577T>A		intron_variant		5	NM_001098816.3	P1
TENM4	ENST00000529798.1	n.400-23354T>A		intron_variant, non_coding_transcript_variant		3
TENM4	ENST00000533013.1	n.77+14043T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13640 AN: 152078 Hom.: 1069 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0899 AC: 13687 AN: 152196 Hom.: 1073 Cov.: 33 AF XY: 0.0906 AC XY: 6743 AN XY: 74418

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0145

Gnomad4 NFE AF: 0.0301

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.0569 Hom.: 68

Bravo AF: 0.0969

Asia WGS AF: 0.197 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.011
Dann	Benign	0.40

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: rs11826937; hg19: chr11-78659145;