rs2577704

chr2-23369274-G-A

Variant summary

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

The XR_939829.4(LINC02923):n.4335+5366C>T 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 0.0991 in 151,506 control chromosomes in the GnomAD database, including 771 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 0.099 (771 hom., cov: 31)
• Consequence: LINC02923 XR_939829.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

LINC02923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02923	XR_939829.4	n.4335+5366C>T		intron_variant, non_coding_transcript_variant
LINC02923	XR_001739338.3	n.5196+5747C>T		intron_variant, non_coding_transcript_variant
LINC02923	XR_939828.4	n.4478+5366C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0990 AC: 14994 AN: 151388 Hom.: 767 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0711

Gnomad ASJ AF: 0.0846

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0991 AC: 15017 AN: 151506 Hom.: 771 Cov.: 31 AF XY: 0.0991 AC XY: 7333 AN XY: 74020

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0711

Gnomad4 ASJ AF: 0.0846

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.0916 Hom.: 1050

Bravo AF: 0.102

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.097
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577704; hg19: chr2-23592145;