chr3-55233363-A-G

Position:

• chr3-55233363-A-G

Variant summary

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

The ENST00000654581.1(LINC02030):​n.362+4A>G variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,128 control chromosomes in the GnomAD database, including 55,897 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 0.85 (55897 hom., cov: 31)
• Consequence: LINC02030 ENST00000654581.1 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

Genes affected

LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)

LOC124906243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.352+2506A>G		intron_variant, non_coding_transcript_variant
LOC124906243	XR_007095917.1	n.158+33499T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+4A>G		splice_donor_region_variant, intron_variant, non_coding_transcript_variant
LINC02030	ENST00000662390.1	n.320+4A>G		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129874 AN: 152010 Hom.: 55867 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.854 AC: 129962 AN: 152128 Hom.: 55897 Cov.: 31 AF XY: 0.860 AC XY: 63987 AN XY: 74376

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.868

Alfa AF: 0.876 Hom.: 97342

Bravo AF: 0.849

Asia WGS AF: 0.962 AC: 3347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs381062; hg19: chr3-55267391;