rs976730

Positions:

• chr9-22695668-T-A
• chr9-22695668-T-C
• chr9-22695668-T-G

Variant summary

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

The XR_001746635.2(LOC107987054):​n.11090A>T 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 0.746 in 151,556 control chromosomes in the GnomAD database, including 42,749 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 0.75 (42749 hom., cov: 32)
• Consequence: LOC107987054 XR_001746635.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

Genes affected

LOC107987054 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987054	XR_001746635.2	n.11090A>T		non_coding_transcript_exon_variant	1/3
LINC01239	NR_038977.1	n.402+12955T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01239	ENST00000436786.1	n.402+12955T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.746 AC: 112909 AN: 151438 Hom.: 42709 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.746 AC: 113008 AN: 151556 Hom.: 42749 Cov.: 32 AF XY: 0.739 AC XY: 54724 AN XY: 74076

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.764

Alfa AF: 0.727 Hom.: 5039

Bravo AF: 0.761

Asia WGS AF: 0.693 AC: 2408 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs976730; hg19: chr9-22695667;