chr2-238640115-A-G

Position:

• chr2-238640115-A-G

Variant summary

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

The ENST00000653335.1(LINC01937):​n.193+69299A>G 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 0.251 in 152,110 control chromosomes in the GnomAD database, including 5,984 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 0.25 (5984 hom., cov: 33)
• Consequence: LINC01937 ENST00000653335.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

LINC01937 (HGNC:52760): (long intergenic non-protein coding RNA 1937)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01937	ENST00000653335.1	n.193+69299A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38175 AN: 151992 Hom.: 5977 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.251 AC: 38211 AN: 152110 Hom.: 5984 Cov.: 33 AF XY: 0.252 AC XY: 18771 AN XY: 74378

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.218

Alfa AF: 0.198 Hom.: 644

Bravo AF: 0.267

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6755528; hg19: chr2-239548756;