rs10511861

chr9-30470776-T-Achr9-30470776-T-C

Variant summary

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

The ENST00000629369.1(LINC01242):n.631-23965A>T 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 0.0479 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01242	ENST00000629369.1	n.631-23965A>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.0553

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0237

Gnomad4 FIN AF: 0.0637

Gnomad4 NFE AF: 0.0176

Gnomad4 OTH AF: 0.0355

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511861; hg19: chr9-30470774;