rs4654432

Variant names:

• chr1-4421155-C-T
• rs4654432
• ENST00000423197.2:n.855-1605C>T

Variant summary

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

The ENST00000423197.2(LINC01777):​n.855-1605C>T variant causes a intron 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 ENST00000423197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423197.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01777	NR_027088.1		n.855-1605C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01777	ENST00000423197.2	TSL:2	n.855-1605C>T		intron	N/A
	LINC01777	ENST00000635002.1	TSL:5	n.596-2193C>T		intron	N/A
	LINC01777	ENST00000635312.2	TSL:5	n.581-1899C>T		intron	N/A

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

African (AFR) AF: 0.361 AC: 14907 AN: 41348

American (AMR) AF: 0.321 AC: 4897 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1694 AN: 3466

East Asian (EAS) AF: 0.103 AC: 531 AN: 5160

South Asian (SAS) AF: 0.291 AC: 1398 AN: 4810

European-Finnish (FIN) AF: 0.441 AC: 4578 AN: 10386

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32214 AN: 67884

Other (OTH) AF: 0.415 AC: 873 AN: 2104

Alfa AF: 0.451 Hom.: 67594

Bravo AF: 0.396

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4654432;

hg19: chr1-4481215;