13-30169232-T-C

Variant names:

• chr13-30169232-T-C
• rs1073230
• NR_187532.1:n.*201T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187532.1(LINC00385):​n.*201T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,046 control chromosomes in the GnomAD database, including 29,744 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 0.62 (29744 hom., cov: 32)
• Consequence: LINC00385 NR_187532.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 4 publications found

Genes affected

LINC00385 (HGNC:42713): (long intergenic non-protein coding RNA 385)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187532.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00385	NR_187532.1		n.*201T>C		downstream_gene	N/A
	LINC00385	NR_187533.1		n.*201T>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94772 AN: 151928 Hom.: 29711 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.624 AC: 94849 AN: 152046 Hom.: 29744 Cov.: 32 AF XY: 0.625 AC XY: 46452 AN XY: 74330

African (AFR) AF: 0.610 AC: 25287 AN: 41464

American (AMR) AF: 0.657 AC: 10042 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3314 AN: 5174

South Asian (SAS) AF: 0.541 AC: 2604 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6488 AN: 10554

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42761 AN: 67972

Other (OTH) AF: 0.609 AC: 1285 AN: 2110

Alfa AF: 0.620 Hom.: 3601

Bravo AF: 0.626

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.46
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1073230; hg19: chr13-30743369;