rs349403

chr1-4413942-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027088.1(LINC01777):n.582+1310A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,124 control chromosomes in the GnomAD database, including 1,226 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 0.12 (1226 hom., cov: 33)
• Consequence: LINC01777 NR_027088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

LINC01777 (HGNC:52567): (long intergenic non-protein coding RNA 1777)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01777	NR_027088.1	n.582+1310A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01777	ENST00000635002.1	n.323+1593A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17878 AN: 152006 Hom.: 1226 Cov.: 33

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.118 AC: 17878 AN: 152124 Hom.: 1226 Cov.: 33 AF XY: 0.116 AC XY: 8598 AN XY: 74380

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.129

Alfa AF: 0.148 Hom.: 789

Bravo AF: 0.112

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.5
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs349403; hg19: chr1-4474002;