rs7553005

chr1-231593864-G-Achr1-231593864-G-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.526-22780G>A 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 0.513 in 147,666 control chromosomes in the GnomAD database, including 20,545 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 0.51 (20545 hom., cov: 23)
• Consequence: TSNAX-DISC1 NR_028393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSNAX-DISC1	NR_028393.1	n.526-22780G>A		intron_variant, non_coding_transcript_variant
LINC00582	NR_034037.1	n.89-2064C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00582	ENST00000448058.1	n.89-2064C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 75733 AN: 147554 Hom.: 20550 Cov.: 23

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.513 AC: 75743 AN: 147666 Hom.: 20545 Cov.: 23 AF XY: 0.518 AC XY: 37163 AN XY: 71794

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.540

Alfa AF: 0.403 Hom.: 994

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7553005; hg19: chr1-231729610;