4-165753164-G-A

Position:

• chr4-165753164-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121676.1(LINC01179):​n.455-1637G>A variant causes a intron, non coding transcript 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 NR_121676.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01179	NR_121676.1	n.455-1637G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01179	ENST00000507838.1	n.455-1637G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000668379.1	n.105+4399C>T		intron_variant, non_coding_transcript_variant
	ENST00000657783.1	n.98+4399C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.355

Alfa AF: 0.370 Hom.: 1418

Bravo AF: 0.320

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs355191; hg19: chr4-166674316;