1-55862923-G-T

Variant names:

• chr1-55862923-G-T
• rs4926698
• ENST00000424357.1:n.367-9G>T

Variant summary

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

The ENST00000424357.1(LINC01755):​n.367-9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,800 control chromosomes in the GnomAD database, including 15,702 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 0.45 (15702 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01755 ENST00000424357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01755	ENST00000424357.1	TSL:3	n.367-9G>T		intron	N/A
	LINC01755	ENST00000646266.1		n.357+15386G>T		intron	N/A
	LINC01755	ENST00000659410.1		n.376+15386G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68110 AN: 151682 Hom.: 15686 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.448

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.449 AC: 68156 AN: 151800 Hom.: 15702 Cov.: 32 AF XY: 0.444 AC XY: 32914 AN XY: 74178

African (AFR) AF: 0.395 AC: 16366 AN: 41384

American (AMR) AF: 0.573 AC: 8738 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3464

East Asian (EAS) AF: 0.271 AC: 1397 AN: 5162

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4816

European-Finnish (FIN) AF: 0.382 AC: 4019 AN: 10518

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33071 AN: 67896

Other (OTH) AF: 0.442 AC: 934 AN: 2112

Alfa AF: 0.485 Hom.: 4465

Bravo AF: 0.459

Asia WGS AF: 0.338 AC: 1170 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.55
PhyloP100		0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4926698;

hg19: chr1-56328596;