rs10888935

Variant names:

• chr1-55595278-T-A
• rs10888935
• ENST00000422374.1:n.158+14084T>A

Variant summary

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

The ENST00000422374.1(LINC01755):​n.158+14084T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,890 control chromosomes in the GnomAD database, including 22,472 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 0.52 (22472 hom., cov: 31)
• Consequence: LINC01755 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

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

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	ENST00000422374.1	TSL:2	n.158+14084T>A		intron	N/A
	LINC01755	ENST00000634769.2	TSL:5	n.134+14084T>A		intron	N/A
	LINC01755	ENST00000643167.1		n.139-19643T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79471 AN: 151772 Hom.: 22460 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.524 AC: 79518 AN: 151890 Hom.: 22472 Cov.: 31 AF XY: 0.524 AC XY: 38881 AN XY: 74206

African (AFR) AF: 0.293 AC: 12133 AN: 41430

American (AMR) AF: 0.643 AC: 9810 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2190 AN: 3462

East Asian (EAS) AF: 0.581 AC: 3000 AN: 5162

South Asian (SAS) AF: 0.605 AC: 2903 AN: 4800

European-Finnish (FIN) AF: 0.503 AC: 5298 AN: 10532

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42268 AN: 67942

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.566 Hom.: 3164

Bravo AF: 0.520

Asia WGS AF: 0.591 AC: 2055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.32
PhyloP100		-0.70

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: rs10888935;

hg19: chr1-56060951;