9-22819577-G-C

Position:

• chr9-22819577-G-C

Variant summary

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

The ENST00000436786.1(LINC01239):​n.525-1161G>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 ENST00000436786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

LINC01239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01239	NR_038977.1	n.525-1161G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01239	ENST00000436786.1	n.525-1161G>C		intron_variant		2
ENSG00000284418	ENST00000640003.1	n.558+2441C>G		intron_variant		5

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

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.691

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849973; hg19: chr9-22819576;