rs17023457

Positions:

• chr1-119333107-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_146623.1(LINC01780):​n.82+4318T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.155 in 152,208 control chromosomes in the GnomAD database, including 2,580 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 0.15 (2580 hom., cov: 33)
• Consequence: LINC01780 NR_146623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.90

Genes affected

LINC01780 (HGNC:52570): (long intergenic non-protein coding RNA 1780)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01780	NR_146623.1	n.82+4318T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01780	ENST00000457683.1	n.82+4318T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23533 AN: 152090 Hom.: 2581 Cov.: 33

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23530 AN: 152208 Hom.: 2580 Cov.: 33 AF XY: 0.159 AC XY: 11828 AN XY: 74448

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.151

Alfa AF: 0.169 Hom.: 3624

Bravo AF: 0.164

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	20
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17023457; hg19: chr1-119875730;