rs2945756

Positions:

• chr8-133673822-A-G
• chr8-133673822-A-T

Variant summary

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

The NR_134462.1(LINC03024):​n.99-8847T>C variant causes a intron, non coding transcript 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 NR_134462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03024	NR_134462.1	n.99-8847T>C		intron_variant, non_coding_transcript_variant
LINC03024	NR_134463.1	n.180-8847T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03024	ENST00000701552.1	n.160-8847T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.759

Alfa AF: 0.705 Hom.: 78829

Bravo AF: 0.749

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2945756; hg19: chr8-134686065;