rs11206628

Variant names:

• chr1-55595308-C-T
• rs11206628
• ENST00000422374.1:n.158+14114C>T

Variant summary

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

The ENST00000422374.1(LINC01755):​n.158+14114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,912 control chromosomes in the GnomAD database, including 22,442 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 (22442 hom., cov: 31)
• Consequence: LINC01755 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01755	ENST00000422374.1	n.158+14114C>T		intron_variant	Intron 1 of 2	2
LINC01755	ENST00000634769.2	n.134+14114C>T		intron_variant	Intron 1 of 3	5
LINC01755	ENST00000643167.1	n.139-19613C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79416 AN: 151794 Hom.: 22433 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.632

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: 0.523 AC: 79459 AN: 151912 Hom.: 22442 Cov.: 31 AF XY: 0.523 AC XY: 38851 AN XY: 74216

African (AFR) AF: 0.291 AC: 12066 AN: 41440

American (AMR) AF: 0.643 AC: 9805 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3466

East Asian (EAS) AF: 0.581 AC: 3001 AN: 5162

South Asian (SAS) AF: 0.605 AC: 2910 AN: 4812

European-Finnish (FIN) AF: 0.503 AC: 5297 AN: 10522

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

European-Non Finnish (NFE) AF: 0.622 AC: 42269 AN: 67940

Other (OTH) AF: 0.542 AC: 1146 AN: 2114

Alfa AF: 0.560 Hom.: 4942

Bravo AF: 0.520

Asia WGS AF: 0.591 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.21
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11206628; hg19: chr1-56060981;