rs430306

Variant names:

• chr1-112109397-G-A
• rs430306
• ENST00000748382.1:n.302-13838C>T

Variant summary

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

The ENST00000748382.1(LINC02884):​n.302-13838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 151,892 control chromosomes in the GnomAD database, including 49,588 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 0.80 (49588 hom., cov: 32)
• Consequence: LINC02884 ENST00000748382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 0 publications found

Genes affected

LINC02884 (HGNC:54808): (long intergenic non-protein coding RNA 2884)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748382.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02884	ENST00000748382.1		n.302-13838C>T		intron	N/A
	LINC02884	ENST00000748397.1		n.439-13838C>T		intron	N/A
	LINC02884	ENST00000748398.1		n.583-13838C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122140 AN: 151772 Hom.: 49549 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.805 AC: 122237 AN: 151892 Hom.: 49588 Cov.: 32 AF XY: 0.805 AC XY: 59708 AN XY: 74198

African (AFR) AF: 0.886 AC: 36756 AN: 41472

American (AMR) AF: 0.763 AC: 11637 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3468

East Asian (EAS) AF: 0.992 AC: 5108 AN: 5148

South Asian (SAS) AF: 0.832 AC: 4007 AN: 4818

European-Finnish (FIN) AF: 0.753 AC: 7920 AN: 10524

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51772 AN: 67904

Other (OTH) AF: 0.777 AC: 1642 AN: 2112

Alfa AF: 0.800 Hom.: 7954

Bravo AF: 0.805

Asia WGS AF: 0.895 AC: 3111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.55
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs430306; hg19: chr1-112652019;