4-165754369-G-C

Variant names:

• chr4-165754369-G-C
• rs355189
• ENST00000507838.1:n.455-432G>C

Variant summary

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

The ENST00000507838.1(LINC01179):​n.455-432G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,184 control chromosomes in the GnomAD database, including 61,929 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 0.90 (61929 hom., cov: 32)
• Consequence: LINC01179 ENST00000507838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 0 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01179	NR_121676.1	n.455-432G>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01179	ENST00000507838.1	n.455-432G>C		intron_variant	Intron 4 of 5	1
ENSG00000287424	ENST00000657783.2	n.546+3194C>G		intron_variant	Intron 1 of 2
ENSG00000287424	ENST00000668379.1	n.105+3194C>G		intron_variant	Intron 1 of 2
ENSG00000287424	ENST00000727691.1	n.105+3194C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136164 AN: 152066 Hom.: 61885 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.895 AC: 136262 AN: 152184 Hom.: 61929 Cov.: 32 AF XY: 0.899 AC XY: 66883 AN XY: 74424

African (AFR) AF: 0.728 AC: 30184 AN: 41440

American (AMR) AF: 0.934 AC: 14280 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3271 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5182

South Asian (SAS) AF: 0.990 AC: 4781 AN: 4828

European-Finnish (FIN) AF: 0.979 AC: 10406 AN: 10624

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65077 AN: 68024

Other (OTH) AF: 0.898 AC: 1900 AN: 2116

Alfa AF: 0.920 Hom.: 8076

Bravo AF: 0.883

Asia WGS AF: 0.978 AC: 3397 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.54
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs355189; hg19: chr4-166675521;