1-55930636-T-C

Variant names:

• chr1-55930636-T-C
• rs12744110
• ENST00000458145.2:n.60-9225A>G

Variant summary

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

The ENST00000458145.2(LINC01753):​n.60-9225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,886 control chromosomes in the GnomAD database, including 35,927 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 0.68 (35927 hom., cov: 31)
• Consequence: LINC01753 ENST00000458145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 1 publications found

Genes affected

LINC01753 (HGNC:52541): (long intergenic non-protein coding RNA 1753)

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01753	NR_147162.1	n.49-9225A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01753	ENST00000458145.2	n.60-9225A>G		intron_variant	Intron 1 of 2	3
LINC01753	ENST00000635532.1	n.59+14280A>G		intron_variant	Intron 1 of 1	5
LINC01755	ENST00000646266.1	n.358-31247T>C		intron_variant	Intron 3 of 11

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103041 AN: 151768 Hom.: 35925 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.679 AC: 103079 AN: 151886 Hom.: 35927 Cov.: 31 AF XY: 0.680 AC XY: 50474 AN XY: 74258

African (AFR) AF: 0.504 AC: 20840 AN: 41352

American (AMR) AF: 0.700 AC: 10689 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4550 AN: 5146

South Asian (SAS) AF: 0.715 AC: 3442 AN: 4812

European-Finnish (FIN) AF: 0.718 AC: 7582 AN: 10560

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.752 AC: 51126 AN: 67956

Other (OTH) AF: 0.703 AC: 1483 AN: 2110

Alfa AF: 0.674 Hom.: 5284

Bravo AF: 0.671

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.95
DANN	Benign	0.89
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs12744110; hg19: chr1-56396309;