rs4654432

chr1-4421155-C-T

Variant summary

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

The NR_027088.1(LINC01777):n.855-1605C>T 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 0.407 in 151,608 control chromosomes in the GnomAD database, including 13,187 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 0.41 (13187 hom., cov: 31)
• Consequence: LINC01777 NR_027088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01777	NR_027088.1	n.855-1605C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01777	ENST00000635002.1	n.596-2193C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61675 AN: 151502 Hom.: 13186 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.407 AC: 61697 AN: 151608 Hom.: 13187 Cov.: 31 AF XY: 0.400 AC XY: 29636 AN XY: 74044

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.415

Alfa AF: 0.458 Hom.: 34019

Bravo AF: 0.396

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4654432; hg19: chr1-4481215;