chr4-165753360-G-A

Variant names:

• chr4-165753360-G-A
• rs191644
• ENST00000507838.1:n.455-1441G>A

Variant summary

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

The ENST00000507838.1(LINC01179):​n.455-1441G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,978 control chromosomes in the GnomAD database, including 10,091 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 0.34 (10091 hom., cov: 32)
• Consequence: LINC01179 ENST00000507838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 4 publications found

Genes affected

LINC01179 (HGNC:49556): (long intergenic non-protein coding RNA 1179)

ENSG00000287424 (HGNC:):

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 = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507838.1. 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
	LINC01179	NR_121676.1		n.455-1441G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01179	ENST00000507838.1	TSL:1	n.455-1441G>A		intron	N/A
	ENSG00000287424	ENST00000657783.2		n.546+4203C>T		intron	N/A
	ENSG00000287424	ENST00000668379.1		n.105+4203C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51381 AN: 151860 Hom.: 10085 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.338 AC: 51402 AN: 151978 Hom.: 10091 Cov.: 32 AF XY: 0.345 AC XY: 25611 AN XY: 74296

African (AFR) AF: 0.142 AC: 5882 AN: 41440

American (AMR) AF: 0.398 AC: 6078 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1175 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1417 AN: 5164

South Asian (SAS) AF: 0.245 AC: 1183 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5644 AN: 10552

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28768 AN: 67942

Other (OTH) AF: 0.363 AC: 766 AN: 2110

Alfa AF: 0.394 Hom.: 55658

Bravo AF: 0.323

Asia WGS AF: 0.261 AC: 912 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	3.5
DANN	Benign	0.66
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs191644; hg19: chr4-166674512;