rs613391

Variant names:

• chr9-22670716-C-G
• rs613391
• ENST00000436786.2:n.196-3727C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-22670716-C-G
• chr9-22670716-C-T

Variant summary

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

The ENST00000436786.2(LINC01239):​n.196-3727C>G variant causes a intron 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 ENST00000436786.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 16 publications found

Genes affected

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

LINC03142 (HGNC:58153):

LOC107987054 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.98-3727C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01239	ENST00000436786.2	TSL:2	n.196-3727C>G		intron	N/A
	LINC03142	ENST00000764217.1		n.623+1792G>C		intron	N/A
	LINC03142	ENST00000764218.1		n.510+1792G>C		intron	N/A

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

African (AFR) AF: 0.878 AC: 36419 AN: 41480

American (AMR) AF: 0.768 AC: 11672 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2582 AN: 3460

East Asian (EAS) AF: 0.606 AC: 3095 AN: 5104

South Asian (SAS) AF: 0.717 AC: 3444 AN: 4804

European-Finnish (FIN) AF: 0.656 AC: 6916 AN: 10548

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 49913 AN: 67812

Other (OTH) AF: 0.782 AC: 1645 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.15
DANN	Benign	0.38
PhyloP100		-0.24

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: rs613391;

hg19: chr9-22670715;