chr1-55523741-T-G

Variant names:

• chr1-55523741-T-G
• rs904610
• ENST00000643167.1:n.139-91180T>G

Variant summary

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

The ENST00000643167.1(LINC01755):​n.139-91180T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,034 control chromosomes in the GnomAD database, including 34,468 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 0.66 (34468 hom., cov: 32)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643167.1. 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
	LINC01755	ENST00000643167.1		n.139-91180T>G		intron	N/A
	LINC01755	ENST00000646341.1		n.159-91180T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101023 AN: 151916 Hom.: 34455 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.665 AC: 101079 AN: 152034 Hom.: 34468 Cov.: 32 AF XY: 0.664 AC XY: 49330 AN XY: 74316

African (AFR) AF: 0.512 AC: 21236 AN: 41454

American (AMR) AF: 0.684 AC: 10454 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2529 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2990 AN: 5174

South Asian (SAS) AF: 0.548 AC: 2636 AN: 4812

European-Finnish (FIN) AF: 0.783 AC: 8270 AN: 10560

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50805 AN: 67968

Other (OTH) AF: 0.653 AC: 1380 AN: 2112

Alfa AF: 0.660 Hom.: 3885

Bravo AF: 0.651

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs904610; hg19: chr1-55989414;