rs72669744

Variant names:

• chr1-55650832-C-T
• rs72669744
• ENST00000422374.1:n.240+35830C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000422374.1(LINC01755):​n.240+35830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0283 in 152,322 control chromosomes in the GnomAD database, including 65 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 0.028 (65 hom., cov: 33)
• Consequence: LINC01755 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 14 publications found

Genes affected

LINC01755 (HGNC:52543): (long intergenic non-protein coding RNA 1755)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0283 (4308/152322) while in subpopulation SAS AF = 0.0509 (246/4834). AF 95% confidence interval is 0.0457. There are 65 homozygotes in GnomAd4. There are 2145 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422374.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01755	ENST00000422374.1	TSL:2	n.240+35830C>T		intron	N/A
	LINC01755	ENST00000634769.2	TSL:5	n.217-22428C>T		intron	N/A
	LINC01755	ENST00000643167.1		n.221-22428C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 4312 AN: 152204 Hom.: 65 Cov.: 33

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0283 AC: 4308 AN: 152322 Hom.: 65 Cov.: 33 AF XY: 0.0288 AC XY: 2145 AN XY: 74484

African (AFR) AF: 0.0325 AC: 1350 AN: 41570

American (AMR) AF: 0.0262 AC: 401 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5186

South Asian (SAS) AF: 0.0509 AC: 246 AN: 4834

European-Finnish (FIN) AF: 0.0268 AC: 285 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0242 AC: 1646 AN: 68028

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.0252 Hom.: 145

Bravo AF: 0.0288

Asia WGS AF: 0.0280 AC: 96 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs72669744; hg19: chr1-56116505;