ENST00000629369.1:n.631-23965A>T

Variant names:

• chr9-30470776-T-A
• rs10511861
• ENST00000629369.1:n.631-23965A>T

Variant summary

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

The ENST00000629369.1(LINC01242):​n.631-23965A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,030 control chromosomes in the GnomAD database, including 351 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 0.048 (351 hom., cov: 31)
• Consequence: LINC01242 ENST00000629369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 1 publications found

Genes affected

LINC01242 (HGNC:49810): (long intergenic non-protein coding RNA 1242)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01242	ENST00000629369.1	n.631-23965A>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 7267 AN: 151912 Hom.: 351 Cov.: 31

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0239

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0479 AC: 7284 AN: 152030 Hom.: 351 Cov.: 31 AF XY: 0.0497 AC XY: 3690 AN XY: 74316

African (AFR) AF: 0.0737 AC: 3055 AN: 41452

American (AMR) AF: 0.0553 AC: 845 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1273 AN: 5148

South Asian (SAS) AF: 0.0237 AC: 114 AN: 4806

European-Finnish (FIN) AF: 0.0637 AC: 673 AN: 10564

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0176 AC: 1200 AN: 67990

Other (OTH) AF: 0.0355 AC: 75 AN: 2114

Alfa AF: 0.00850 Hom.: 3

Bravo AF: 0.0535

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.68
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10511861; hg19: chr9-30470774;