rs1914369

Positions:

• chr4-181859415-G-A
• chr4-181859415-G-C
• chr4-181859415-G-T

Variant summary

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

The XM_017008385.2(TENM3):​c.-236-8337G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 151,948 control chromosomes in the GnomAD database, including 46,271 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 (46271 hom., cov: 30)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

Genes affected

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3	XM_017008385.2	c.-236-8337G>A		intron_variant			XP_016863874.1
TENM3	XM_017008389.2	c.-236-8337G>A		intron_variant			XP_016863878.1
TENM3	XM_017008390.2	c.-236-8337G>A		intron_variant			XP_016863879.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118080 AN: 151830 Hom.: 46229 Cov.: 30

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.778 AC: 118179 AN: 151948 Hom.: 46271 Cov.: 30 AF XY: 0.780 AC XY: 57892 AN XY: 74240

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.772

Alfa AF: 0.746 Hom.: 71007

Bravo AF: 0.781

Asia WGS AF: 0.891 AC: 3100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1914369; hg19: chr4-182780568;