2-238581169-G-C

Position:

• chr2-238581169-G-C

Variant summary

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

The ENST00000653335.1(LINC01937):​n.193+10353G>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 0.298 in 152,100 control chromosomes in the GnomAD database, including 6,926 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 0.30 (6926 hom., cov: 32)
• Consequence: LINC01937 ENST00000653335.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01937	ENST00000653335.1	n.193+10353G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45251 AN: 151978 Hom.: 6927 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.298 AC: 45271 AN: 152100 Hom.: 6926 Cov.: 32 AF XY: 0.293 AC XY: 21801 AN XY: 74342

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.301

Alfa AF: 0.308 Hom.: 901

Bravo AF: 0.289

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6751336; hg19: chr2-239489810;