rs1615409

Positions:

• chr1-231547671-C-A
• chr1-231547671-C-G
• chr1-231547671-C-T

Variant summary

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

The NM_005999.3(TSNAX):​c.367+5060C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 150,978 control chromosomes in the GnomAD database, including 19,032 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 (19032 hom., cov: 30)
• Consequence: TSNAX NM_005999.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

TSNAX (HGNC:12380): (translin associated factor X) This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs. [provided by RefSeq, Jul 2008]

TSNAX-DISC1 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSNAX	NM_005999.3	c.367+5060C>A		intron_variant		ENST00000366639.9
TSNAX-DISC1	NR_028393.1	n.525+5060C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSNAX	ENST00000366639.9	c.367+5060C>A		intron_variant		1	NM_005999.3	P1
TSNAX	ENST00000413309.3	c.388+5060C>A		intron_variant		3
TSNAX	ENST00000475168.1	n.3339+5060C>A		intron_variant, non_coding_transcript_variant		2
TSNAX	ENST00000602825.5	n.511+5060C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72247 AN: 150858 Hom.: 18974 Cov.: 30

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.479 AC: 72371 AN: 150978 Hom.: 19032 Cov.: 30 AF XY: 0.473 AC XY: 34867 AN XY: 73722

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.464

Alfa AF: 0.416 Hom.: 1717

Bravo AF: 0.507

Asia WGS AF: 0.498 AC: 1732 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.080
DANN	Benign	0.35

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: rs1615409; hg19: chr1-231683417; COSMIC: COSV64146048; COSMIC: COSV64146048;