rs6701127

Variant names:

• chr1-175120958-A-G
• rs6701127
• NM_022093.2:c.2650+2134A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-175120958-A-G
• chr1-175120958-A-T

Variant summary

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

The NM_022093.2(TNN):​c.2650+2134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,856 control chromosomes in the GnomAD database, including 17,914 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 0.48 (17914 hom., cov: 32)
• Consequence: TNN NM_022093.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

TNN (HGNC:22942): (tenascin N) Predicted to enable integrin binding activity. Predicted to be involved in several processes, including generation of neurons; negative regulation of canonical Wnt signaling pathway involved in osteoblast differentiation; and negative regulation of osteoblast differentiation. Predicted to act upstream of or within axonogenesis. Predicted to be located in extracellular matrix and neuron projection. Predicted to be active in collagen-containing extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNN	NM_022093.2	c.2650+2134A>G		intron_variant	Intron 11 of 18	ENST00000239462.9	NP_071376.1
TNN	XM_017002048.2	c.2704+2134A>G		intron_variant	Intron 11 of 18		XP_016857537.1
TNN	XM_017002049.2	c.2441-2442A>G		intron_variant	Intron 10 of 17		XP_016857538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNN	ENST00000239462.9	c.2650+2134A>G		intron_variant	Intron 11 of 18	2	NM_022093.2	ENSP00000239462.4
TNN	ENST00000621086.1	c.2119+2134A>G		intron_variant	Intron 8 of 15	5		ENSP00000480895.1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73129 AN: 151736 Hom.: 17893 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.482 AC: 73189 AN: 151856 Hom.: 17914 Cov.: 32 AF XY: 0.490 AC XY: 36375 AN XY: 74250

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.498

Alfa AF: 0.459 Hom.: 16175

Bravo AF: 0.487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.11

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: rs6701127; hg19: chr1-175090094;