rs4968382

Variant names:

• chr17-59515354-G-A
• rs4968382
• ENST00000577478.2:n.393+11126C>T

Variant summary

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

The ENST00000577478.2(LINC01476):​n.393+11126C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,866 control chromosomes in the GnomAD database, including 18,555 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 0.43 (18555 hom., cov: 31)
• Consequence: LINC01476 ENST00000577478.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 6 publications found

Genes affected

LINC01476 (HGNC:51117): (long intergenic non-protein coding RNA 1476)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577478.2. 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
	LINC01476	NR_110813.1		n.378+11126C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01476	ENST00000577478.2	TSL:4	n.393+11126C>T		intron	N/A
	LINC01476	ENST00000584262.6	TSL:4	n.467+11126C>T		intron	N/A
	LINC01476	ENST00000654551.1		n.378+11126C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65610 AN: 151748 Hom.: 18488 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.433 AC: 65720 AN: 151866 Hom.: 18555 Cov.: 31 AF XY: 0.435 AC XY: 32269 AN XY: 74182

African (AFR) AF: 0.794 AC: 32924 AN: 41450

American (AMR) AF: 0.380 AC: 5793 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3472

East Asian (EAS) AF: 0.548 AC: 2830 AN: 5168

South Asian (SAS) AF: 0.473 AC: 2271 AN: 4804

European-Finnish (FIN) AF: 0.280 AC: 2937 AN: 10500

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16569 AN: 67934

Other (OTH) AF: 0.407 AC: 859 AN: 2108

Alfa AF: 0.358 Hom.: 2238

Bravo AF: 0.451

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		-0.58

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: rs4968382;

hg19: chr17-57592715;