chr9-22740233-G-A

Variant names:

• chr9-22740233-G-A
• rs7872081
• ENST00000764223.1:n.1528C>T

Variant summary

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

The ENST00000764223.1(ENSG00000284418):​n.1528C>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 0.0877 in 152,066 control chromosomes in the GnomAD database, including 753 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 0.088 (753 hom., cov: 32)
• Consequence: ENSG00000284418 ENST00000764223.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• Publications: 2 publications found

Genes affected

ENSG00000284418 (HGNC:58153):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764223.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01239	NR_038977.1		n.524+16803G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284418	ENST00000764223.1		n.1528C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01239	ENST00000436786.2	TSL:2	n.622+16803G>A		intron	N/A
	ENSG00000284418	ENST00000640003.1	TSL:5	n.960+1145C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13315 AN: 151948 Hom.: 752 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.0455

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0877 AC: 13331 AN: 152066 Hom.: 753 Cov.: 32 AF XY: 0.0871 AC XY: 6470 AN XY: 74322

African (AFR) AF: 0.152 AC: 6289 AN: 41466

American (AMR) AF: 0.0738 AC: 1126 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3464

East Asian (EAS) AF: 0.127 AC: 653 AN: 5144

South Asian (SAS) AF: 0.0810 AC: 391 AN: 4830

European-Finnish (FIN) AF: 0.0455 AC: 482 AN: 10600

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0539 AC: 3668 AN: 67990

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.0496 Hom.: 71

Bravo AF: 0.0944

Asia WGS AF: 0.121 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.54
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7872081; hg19: chr9-22740232;