9-22819577-G-C

Variant names:

• chr9-22819577-G-C
• rs7849973
• ENST00000436786.2:n.623-1161G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436786.2(LINC01239):​n.623-1161G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 151,944 control chromosomes in the GnomAD database, including 37,296 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 0.70 (37296 hom., cov: 31)
• Consequence: LINC01239 ENST00000436786.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 10 publications found

Genes affected

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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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.525-1161G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01239	ENST00000436786.2	TSL:2	n.623-1161G>C		intron	N/A
	LINC03142	ENST00000640003.1	TSL:5	n.558+2441C>G		intron	N/A
	LINC03142	ENST00000764217.1		n.240+54621C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105509 AN: 151826 Hom.: 37245 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.695 AC: 105623 AN: 151944 Hom.: 37296 Cov.: 31 AF XY: 0.692 AC XY: 51382 AN XY: 74248

African (AFR) AF: 0.800 AC: 33157 AN: 41462

American (AMR) AF: 0.592 AC: 9022 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3468

East Asian (EAS) AF: 0.882 AC: 4550 AN: 5156

South Asian (SAS) AF: 0.571 AC: 2746 AN: 4806

European-Finnish (FIN) AF: 0.690 AC: 7274 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44466 AN: 67956

Other (OTH) AF: 0.691 AC: 1456 AN: 2108

Alfa AF: 0.595 Hom.: 1890

Bravo AF: 0.698

Asia WGS AF: 0.721 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.8
DANN	Benign	0.50
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7849973;

hg19: chr9-22819576;