rs10970305

chr9-31372585-A-C

Variant summary

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

The NR_135134.1(LINC01243):n.133-386T>G 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 0.599 in 151,960 control chromosomes in the GnomAD database, including 27,997 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 0.60 (27997 hom., cov: 32)
• Consequence: LINC01243 NR_135134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

LINC01243 (HGNC:49814): (long intergenic non-protein coding RNA 1243)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01243	NR_135134.1	n.133-386T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01243	ENST00000562065.1	n.133-386T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90903 AN: 151842 Hom.: 27937 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.599 AC: 91025 AN: 151960 Hom.: 27997 Cov.: 32 AF XY: 0.607 AC XY: 45044 AN XY: 74250

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.571

Alfa AF: 0.535 Hom.: 4539

Bravo AF: 0.609

Asia WGS AF: 0.758 AC: 2632 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.7
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10970305; hg19: chr9-31372583;