2-242032370-C-A

Position:

• chr2-242032370-C-A

Variant summary

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

The NR_110220.1(LINC01237):​n.314-46090C>A 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 0.534 in 151,018 control chromosomes in the GnomAD database, including 23,142 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 0.53 (23142 hom., cov: 31)
• Consequence: LINC01237 NR_110220.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

Genes affected

LINC01237 (HGNC:49793): (long intergenic non-protein coding RNA 1237)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01237	NR_110220.1	n.314-46090C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01237	ENST00000415434.5	n.311-46090C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80615 AN: 150900 Hom.: 23116 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.534 AC: 80704 AN: 151018 Hom.: 23142 Cov.: 31 AF XY: 0.534 AC XY: 39374 AN XY: 73756

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.532

Alfa AF: 0.392 Hom.: 1641

Bravo AF: 0.558

Asia WGS AF: 0.604 AC: 2099 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	0.74
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12615852; hg19: chr2-242974521;