rs6751336

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653335.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01937	ENST00000653335.1		n.193+10353G>C		intron	N/A
	LINC01937	ENST00000748293.1		n.175+10353G>C		intron	N/A

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

African (AFR) AF: 0.297 AC: 12294 AN: 41460

American (AMR) AF: 0.225 AC: 3439 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3472

East Asian (EAS) AF: 0.130 AC: 675 AN: 5184

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3302 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21924 AN: 67980

Other (OTH) AF: 0.301 AC: 635 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6751336; hg19: chr2-239489810;