1-231626594-G-C

Position:

• chr1-231626594-G-C

Variant summary

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

The NR_028393.1(TSNAX-DISC1):​n.788+9688G>C 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 0.464 in 151,112 control chromosomes in the GnomAD database, including 17,226 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 0.46 (17226 hom., cov: 27)
• Consequence: TSNAX-DISC1 NR_028393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

Genes affected

TSNAX-DISC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSNAX-DISC1	NR_028393.1	n.788+9688G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70142 AN: 150990 Hom.: 17227 Cov.: 27

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.464 AC: 70151 AN: 151112 Hom.: 17226 Cov.: 27 AF XY: 0.464 AC XY: 34274 AN XY: 73806

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.471

Alfa AF: 0.396 Hom.: 1198

Bravo AF: 0.448

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738398; hg19: chr1-231762340; COSMIC: COSV54403256;