rs4654433

Variant names:

• chr1-4421572-G-A
• rs4654433
• ENST00000423197.2:n.855-1188G>A

Variant summary

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

The ENST00000423197.2(LINC01777):​n.855-1188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,054 control chromosomes in the GnomAD database, including 13,991 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 0.42 (13991 hom., cov: 33)
• Consequence: LINC01777 ENST00000423197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt
LINC01777	NR_027088.1	n.855-1188G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01777	ENST00000423197.2	n.855-1188G>A		intron_variant	Intron 3 of 5	2
LINC01777	ENST00000635002.1	n.596-1776G>A		intron_variant	Intron 3 of 4	5
LINC01777	ENST00000635312.2	n.581-1482G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63918 AN: 151934 Hom.: 13984 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.421 AC: 63953 AN: 152054 Hom.: 13991 Cov.: 33 AF XY: 0.413 AC XY: 30714 AN XY: 74334

African (AFR) AF: 0.410 AC: 16992 AN: 41454

American (AMR) AF: 0.324 AC: 4956 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3470

East Asian (EAS) AF: 0.103 AC: 530 AN: 5168

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4828

European-Finnish (FIN) AF: 0.439 AC: 4640 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32236 AN: 67954

Other (OTH) AF: 0.423 AC: 893 AN: 2112

Alfa AF: 0.436 Hom.: 2404

Bravo AF: 0.411

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.094
DANN	Benign	0.35
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4654433; hg19: chr1-4481632;