rs4950322

chr1-147383114-G-A

Variant summary

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

The NR_038423.2(LINC00624):n.2450C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,120 control chromosomes in the GnomAD database, including 2,592 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 0.18 (2592 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00624 NR_038423.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

LINC00624 (HGNC:44254): (long intergenic non-protein coding RNA 624)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00624	NR_038423.2	n.2450C>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00624	ENST00000621316.1	n.2450C>T		non_coding_transcript_exon_variant	4/4	1
LINC00624	ENST00000619867.4	n.996+1554C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27116 AN: 152002 Hom.: 2597 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.185

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.178 AC: 27109 AN: 152120 Hom.: 2592 Cov.: 32 AF XY: 0.177 AC XY: 13176 AN XY: 74366

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0762

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.184

Alfa AF: 0.200 Hom.: 7023

Bravo AF: 0.170

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.34
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4950322; hg19: chr1-146854836;