2-23378685-A-G

Position:

• chr2-23378685-A-G

Variant summary

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

The ENST00000421563.5(LINC02923):​n.80-1759T>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 0.713 in 152,178 control chromosomes in the GnomAD database, including 39,882 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 0.71 (39882 hom., cov: 33)
• Consequence: LINC02923 ENST00000421563.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

LINC02923 (HGNC:55672): (long intergenic non-protein coding RNA 2923)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02923	XR_939829.4	n.3427+2536T>C		intron_variant, non_coding_transcript_variant
LINC02923	XR_001739338.3	n.3428-1759T>C		intron_variant, non_coding_transcript_variant
LINC02923	XR_939828.4	n.3428-1759T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02923	ENST00000421563.5	n.80-1759T>C		intron_variant, non_coding_transcript_variant		4
LINC02923	ENST00000430051.1	n.153+1439T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108425 AN: 152060 Hom.: 39864 Cov.: 33

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.713 AC: 108474 AN: 152178 Hom.: 39882 Cov.: 33 AF XY: 0.717 AC XY: 53365 AN XY: 74402

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.743

Alfa AF: 0.771 Hom.: 26977

Bravo AF: 0.697

Asia WGS AF: 0.817 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577756; hg19: chr2-23601556;