rs528048

chr11-79353581-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.-320-56038G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,082 control chromosomes in the GnomAD database, including 47,057 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 0.78 (47057 hom., cov: 31)
• Consequence: TENM4 NM_001098816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM4	NM_001098816.3	c.-320-56038G>A		intron_variant		ENST00000278550.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM4	ENST00000278550.12	c.-320-56038G>A		intron_variant		5	NM_001098816.3	P1
TENM4	ENST00000528688.5	n.240-56038G>A		intron_variant, non_coding_transcript_variant		3
TENM4	ENST00000531583.1	n.441-56038G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119065 AN: 151964 Hom.: 47000 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.784 AC: 119183 AN: 152082 Hom.: 47057 Cov.: 31 AF XY: 0.782 AC XY: 58092 AN XY: 74322

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.764

Alfa AF: 0.776 Hom.: 5897

Bravo AF: 0.783

Asia WGS AF: 0.675 AC: 2347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	13
Dann	Benign	0.73

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: rs528048; hg19: chr11-79064626;