rs880762

chr11-79346534-C-T

Variant summary

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

The NM_001098816.3(TENM4):c.-320-48991G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,916 control chromosomes in the GnomAD database, including 28,506 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 0.60 (28506 hom., cov: 31)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM4	NM_001098816.3	c.-320-48991G>A		intron_variant		ENST00000278550.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM4	ENST00000278550.12	c.-320-48991G>A		intron_variant		5	NM_001098816.3	P1
TENM4	ENST00000528688.5	n.240-48991G>A		intron_variant, non_coding_transcript_variant		3
TENM4	ENST00000531583.1	n.441-48991G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90490 AN: 151798 Hom.: 28464 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.596 AC: 90588 AN: 151916 Hom.: 28506 Cov.: 31 AF XY: 0.588 AC XY: 43664 AN XY: 74234

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.564

Alfa AF: 0.557 Hom.: 4169

Bravo AF: 0.605

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.87
Dann	Benign	0.53

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: rs880762; hg19: chr11-79057579;