1-55349911-G-A

Variant names:

• chr1-55349911-G-A
• rs207127
• ENST00000643167.1:n.138+20486G>A

Variant summary

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

The ENST00000643167.1(LINC01755):​n.138+20486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,130 control chromosomes in the GnomAD database, including 58,003 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 0.87 (58003 hom., cov: 31)
• Consequence: LINC01755 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.975 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01755	ENST00000643167.1		n.138+20486G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132407 AN: 152012 Hom.: 57952 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.871 AC: 132516 AN: 152130 Hom.: 58003 Cov.: 31 AF XY: 0.874 AC XY: 64986 AN XY: 74364

African (AFR) AF: 0.791 AC: 32791 AN: 41456

American (AMR) AF: 0.912 AC: 13943 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2843 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5154 AN: 5164

South Asian (SAS) AF: 0.945 AC: 4557 AN: 4820

European-Finnish (FIN) AF: 0.906 AC: 9605 AN: 10604

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60719 AN: 68006

Other (OTH) AF: 0.877 AC: 1853 AN: 2114

Alfa AF: 0.889 Hom.: 49694

Bravo AF: 0.868

Asia WGS AF: 0.960 AC: 3335 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	0.28
DANN	Benign	0.61
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs207127; hg19: chr1-55815584;