rs1025526

Positions:

• chr1-231614895-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.526-1749C>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 0.544 in 152,120 control chromosomes in the GnomAD database, including 24,208 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 0.54 (24208 hom., cov: 33)
• Consequence: TSNAX-DISC1 NR_028393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

Genes affected

TSNAX-DISC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSNAX-DISC1	NR_028393.1	n.526-1749C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82749 AN: 152002 Hom.: 24199 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.544 AC: 82777 AN: 152120 Hom.: 24208 Cov.: 33 AF XY: 0.540 AC XY: 40130 AN XY: 74352

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.584

Alfa AF: 0.600 Hom.: 3517

Bravo AF: 0.525

Asia WGS AF: 0.413 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1025526; hg19: chr1-231750641; COSMIC: COSV71449416;