rs6755528

Variant names:

• chr2-238640115-A-G
• rs6755528
• ENST00000653335.1:n.193+69299A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653335.1(LINC01937):​n.193+69299A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 6 publications found

Genes affected

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

ENSG00000297809 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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+69299A>G		intron	N/A
	ENSG00000297809	ENST00000751151.1		n.467-1065A>G		intron	N/A

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

African (AFR) AF: 0.435 AC: 18053 AN: 41474

American (AMR) AF: 0.215 AC: 3283 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2229 AN: 5174

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1539 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10570 AN: 67984

Other (OTH) AF: 0.218 AC: 461 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.48
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6755528; hg19: chr2-239548756;