chr9-22695668-T-A

Variant names:

• chr9-22695668-T-A
• rs976730
• XR_001746635.2:n.11090A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC107987054 (HGNC:):

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

LINC03142 (HGNC:58153):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436786.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01239	NR_038977.1		n.402+12955T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01239	ENST00000436786.2	TSL:2	n.500+12955T>A		intron	N/A
	LINC03142	ENST00000764217.1		n.384-5011A>T		intron	N/A
	LINC03142	ENST00000764218.1		n.384-23034A>T		intron	N/A

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

African (AFR) AF: 0.874 AC: 36232 AN: 41440

American (AMR) AF: 0.751 AC: 11390 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2514 AN: 3454

East Asian (EAS) AF: 0.608 AC: 3125 AN: 5136

South Asian (SAS) AF: 0.692 AC: 3336 AN: 4820

European-Finnish (FIN) AF: 0.590 AC: 6227 AN: 10562

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47788 AN: 67662

Other (OTH) AF: 0.764 AC: 1606 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs976730; hg19: chr9-22695667;