rs613391

chr9-22670716-C-Gchr9-22670716-C-T

Variant summary

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

The NR_038977.1(LINC01239):n.98-3727C>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 0.767 in 151,706 control chromosomes in the GnomAD database, including 45,089 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 0.77 (45089 hom., cov: 30)
• Consequence: LINC01239 NR_038977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

LINC01239 (HGNC:49796): (long intergenic non-protein coding RNA 1239)

LOC107987054 (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 = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01239	NR_038977.1	n.98-3727C>G		intron_variant, non_coding_transcript_variant
LOC107987054	XR_001746635.2	n.16340+1792G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01239	ENST00000436786.1	n.98-3727C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116332 AN: 151588 Hom.: 45049 Cov.: 30

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.767 AC: 116432 AN: 151706 Hom.: 45089 Cov.: 30 AF XY: 0.761 AC XY: 56426 AN XY: 74110

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.782

Alfa AF: 0.736 Hom.: 22940

Bravo AF: 0.778

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.15
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs613391; hg19: chr9-22670715;