rs1655297

chr1-231597941-C-T

Variant summary

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

The NR_028393.1(TSNAX-DISC1):n.526-18703C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,008 control chromosomes in the GnomAD database, including 20,652 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 0.50 (20652 hom., cov: 33)
• Consequence: TSNAX-DISC1 NR_028393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

LINC00582 (HGNC:43842): (long intergenic non-protein coding RNA 582)

TSNAX-DISC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSNAX-DISC1	NR_028393.1	n.526-18703C>T		intron_variant, non_coding_transcript_variant
LINC00582	NR_034037.1	n.89-6141G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00582	ENST00000448058.1	n.89-6141G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75355 AN: 151890 Hom.: 20649 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.496 AC: 75374 AN: 152008 Hom.: 20652 Cov.: 33 AF XY: 0.494 AC XY: 36728 AN XY: 74294

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.546

Alfa AF: 0.557 Hom.: 3094

Bravo AF: 0.468

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.7
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1655297; hg19: chr1-231733687;