chr5-173733681-T-C

Position:

• chr5-173733681-T-C

Variant summary

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

The NR_108027.1(LINC01484):​n.190+12339A>G 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 0.426 in 152,226 control chromosomes in the GnomAD database, including 14,284 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 (14284 hom., cov: 34)
• Consequence: LINC01484 NR_108027.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.73

Genes affected

LINC01484 (HGNC:51136): (long intergenic non-protein coding RNA 1484)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01484	NR_108027.1	n.190+12339A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01484	ENST00000517733.1	n.190+12339A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64792 AN: 152108 Hom.: 14270 Cov.: 34

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.426 AC: 64841 AN: 152226 Hom.: 14284 Cov.: 34 AF XY: 0.423 AC XY: 31498 AN XY: 74430

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.383

Alfa AF: 0.396 Hom.: 6063

Bravo AF: 0.438

Asia WGS AF: 0.484 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.022
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10071956; hg19: chr5-173160684;