chrX-102963359-A-G

Position:

• chrX-102963359-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00630 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00630	NR_146589.1	n.3717A>G		non_coding_transcript_exon_variant	12/12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.200 AC: 22128 AN: 110480 Hom.: 1777 Cov.: 22 AF XY: 0.186 AC XY: 6094 AN XY: 32790

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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.0553

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.176

Alfa AF: 0.199 Hom.: 1285

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945919; hg19: chrX-102218287;