rs10520514

Positions:

• chr4-181861392-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_017008385.2(TENM3):​c.-236-6360T>A variant causes a intron change. The variant allele was found at a frequency of 0.309 in 152,020 control chromosomes in the GnomAD database, including 8,100 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 0.31 (8100 hom., cov: 32)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.26

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-236-6360T>A		intron_variant
TENM3	XM_017008389.2	c.-236-6360T>A		intron_variant
TENM3	XM_017008390.2	c.-236-6360T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46945 AN: 151902 Hom.: 8097 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.309 AC: 46963 AN: 152020 Hom.: 8100 Cov.: 32 AF XY: 0.308 AC XY: 22851 AN XY: 74312

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.317

Alfa AF: 0.353 Hom.: 1216

Bravo AF: 0.301

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10520514; hg19: chr4-182782545;