rs6751336

Variant names:

• chr2-238581169-G-C
• rs6751336
• ENST00000653335.1:n.193+10353G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01937	ENST00000653335.1	n.193+10353G>C		intron_variant	Intron 2 of 2

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;