rs355191

Variant names:

• chr4-165753164-G-A
• rs355191
• ENST00000507838.1:n.455-1637G>A

Variant summary

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

The ENST00000507838.1(LINC01179):​n.455-1637G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,974 control chromosomes in the GnomAD database, including 9,881 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 0.33 (9881 hom., cov: 32)
• Consequence: LINC01179 ENST00000507838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 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.455-1637G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01179	ENST00000507838.1	TSL:1	n.455-1637G>A		intron	N/A
	ENSG00000287424	ENST00000657783.2		n.546+4399C>T		intron	N/A
	ENSG00000287424	ENST00000668379.1		n.105+4399C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50865 AN: 151856 Hom.: 9878 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.335 AC: 50882 AN: 151974 Hom.: 9881 Cov.: 32 AF XY: 0.341 AC XY: 25338 AN XY: 74250

African (AFR) AF: 0.140 AC: 5821 AN: 41482

American (AMR) AF: 0.392 AC: 5988 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1173 AN: 3464

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5162

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5625 AN: 10540

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28441 AN: 67932

Other (OTH) AF: 0.355 AC: 748 AN: 2108

Alfa AF: 0.361 Hom.: 1429

Bravo AF: 0.320

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs355191; hg19: chr4-166674316;