1-60629886-G-C

Variant names:

• chr1-60629886-G-C
• rs472913
• ENST00000439156.2:n.336+10125C>G

Variant summary

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

The ENST00000439156.2(LINC01748):​n.336+10125C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,688 control chromosomes in the GnomAD database, including 16,881 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 0.47 (16881 hom., cov: 31)
• Consequence: LINC01748 ENST00000439156.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 22 publications found

Genes affected

LINC01748 (HGNC:52535): (long intergenic non-protein coding RNA 1748)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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
LINC01748	ENST00000439156.2	n.336+10125C>G		intron_variant	Intron 2 of 7	5
LINC01748	ENST00000661045.1	n.104+10125C>G		intron_variant	Intron 1 of 3
LINC01748	ENST00000662065.1	n.343+10125C>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71196 AN: 151572 Hom.: 16867 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.470 AC: 71230 AN: 151688 Hom.: 16881 Cov.: 31 AF XY: 0.471 AC XY: 34921 AN XY: 74134

African (AFR) AF: 0.461 AC: 19092 AN: 41370

American (AMR) AF: 0.504 AC: 7697 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3285 AN: 5168

South Asian (SAS) AF: 0.581 AC: 2799 AN: 4814

European-Finnish (FIN) AF: 0.411 AC: 4296 AN: 10448

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30800 AN: 67846

Other (OTH) AF: 0.494 AC: 1041 AN: 2106

Alfa AF: 0.283 Hom.: 632

Bravo AF: 0.475

Asia WGS AF: 0.590 AC: 2044 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.60
PhyloP100		-0.19
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs472913; hg19: chr1-61095558;