chr8-133673822-A-G

Variant names:

• chr8-133673822-A-G
• rs2945756
• ENST00000701552.2:n.292-8847T>C

Variant summary

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

The ENST00000701552.2(LINC03024):​n.292-8847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,104 control chromosomes in the GnomAD database, including 42,651 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 0.74 (42651 hom., cov: 32)
• Consequence: LINC03024 ENST00000701552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 4 publications found

Genes affected

LINC03024 (HGNC:56155): (long intergenic non-protein coding RNA 3024)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701552.2. 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
	LINC03024	NR_134462.1		n.99-8847T>C		intron	N/A
	LINC03024	NR_134463.1		n.180-8847T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03024	ENST00000701552.2		n.292-8847T>C		intron	N/A
	LINC03024	ENST00000722577.1		n.200-8847T>C		intron	N/A
	LINC03024	ENST00000722578.1		n.144-3354T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112752 AN: 151984 Hom.: 42594 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.742 AC: 112863 AN: 152104 Hom.: 42651 Cov.: 32 AF XY: 0.739 AC XY: 54964 AN XY: 74366

African (AFR) AF: 0.880 AC: 36546 AN: 41514

American (AMR) AF: 0.710 AC: 10859 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2593 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2874 AN: 5164

South Asian (SAS) AF: 0.743 AC: 3583 AN: 4824

European-Finnish (FIN) AF: 0.632 AC: 6676 AN: 10564

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47143 AN: 67968

Other (OTH) AF: 0.759 AC: 1601 AN: 2108

Alfa AF: 0.706 Hom.: 176024

Bravo AF: 0.749

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2945756; hg19: chr8-134686065;