11-79366149-A-G

Position:

• chr11-79366149-A-G

Variant summary

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

The NM_001098816.3(TENM4):​c.-320-68606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,918 control chromosomes in the GnomAD database, including 1,727 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 0.15 (1727 hom., cov: 32)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM4	NM_001098816.3	c.-320-68606T>C		intron_variant		ENST00000278550.12	NP_001092286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM4	ENST00000278550.12	c.-320-68606T>C		intron_variant		5	NM_001098816.3	ENSP00000278550	P1
TENM4	ENST00000528688.5	n.240-68606T>C		intron_variant, non_coding_transcript_variant		3
TENM4	ENST00000531583.1	n.441-68606T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22370 AN: 151802 Hom.: 1728 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0958

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22372 AN: 151918 Hom.: 1727 Cov.: 32 AF XY: 0.146 AC XY: 10819 AN XY: 74242

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0545

Gnomad4 SAS AF: 0.0683

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.137

Alfa AF: 0.163 Hom.: 3287

Bravo AF: 0.143

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.65

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: rs12576775; hg19: chr11-79077193;