chr1-204061593-A-G

Variant names:

• chr1-204061593-A-G
• rs3911890
• ENST00000745113.1:n.115+12283T>C

Variant summary

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

The ENST00000745113.1(LINC00303):​n.115+12283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,046 control chromosomes in the GnomAD database, including 39,928 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 0.72 (39928 hom., cov: 31)
• Consequence: LINC00303 ENST00000745113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 6 publications found

Genes affected

LINC00303 (HGNC:26865): (long intergenic non-protein coding RNA 303)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745113.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00303	ENST00000745113.1		n.115+12283T>C		intron	N/A
	LINC00303	ENST00000745114.1		n.83+12283T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109870 AN: 151926 Hom.: 39909 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.723 AC: 109943 AN: 152046 Hom.: 39928 Cov.: 31 AF XY: 0.718 AC XY: 53393 AN XY: 74316

African (AFR) AF: 0.678 AC: 28084 AN: 41450

American (AMR) AF: 0.789 AC: 12063 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2796 AN: 3468

East Asian (EAS) AF: 0.718 AC: 3708 AN: 5164

South Asian (SAS) AF: 0.774 AC: 3726 AN: 4812

European-Finnish (FIN) AF: 0.649 AC: 6856 AN: 10556

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50064 AN: 67998

Other (OTH) AF: 0.775 AC: 1636 AN: 2110

Alfa AF: 0.735 Hom.: 189550

Bravo AF: 0.732

Asia WGS AF: 0.740 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.63
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3911890; hg19: chr1-204030721;