chrX-102963359-A-G

Variant names:

• chrX-102963359-A-G
• rs5945919
• NR_146589.1:n.3717A>G

Variant summary

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

The NR_146589.1(LINC00630):​n.3717A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 110,531 control chromosomes in the GnomAD database, including 1,776 homozygotes. There are 6,103 hemizygotes in GnomAD. 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 0.20 (1776 hom., 6103 hem., cov: 22)
• Consequence: LINC00630 NR_146589.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 3 publications found

Genes affected

LINC00630 (HGNC:44263): (long intergenic non-protein coding RNA 630)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146589.1. 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
	LINC00630	NR_146589.1		n.3717A>G		non_coding_transcript_exon	Exon 12 of 12

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00630	ENST00000420471.6	TSL:3	n.1748-33538A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 22128 AN: 110480 Hom.: 1777 Cov.: 22

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.200 AC: 22131 AN: 110531 Hom.: 1776 Cov.: 22 AF XY: 0.186 AC XY: 6103 AN XY: 32851

African (AFR) AF: 0.258 AC: 7754 AN: 30050

American (AMR) AF: 0.129 AC: 1342 AN: 10429

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 345 AN: 2640

East Asian (EAS) AF: 0.0553 AC: 196 AN: 3545

South Asian (SAS) AF: 0.138 AC: 362 AN: 2627

European-Finnish (FIN) AF: 0.140 AC: 826 AN: 5911

Middle Eastern (MID) AF: 0.125 AC: 27 AN: 216

European-Non Finnish (NFE) AF: 0.205 AC: 10872 AN: 52930

Other (OTH) AF: 0.176 AC: 265 AN: 1507

Alfa AF: 0.199 Hom.: 1285

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.43
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs5945919; hg19: chrX-102218287;