rs11045000

Variant names:

• chr12-20031212-G-A
• rs11045000
• ENST00000716354.1:n.4575+11516G>A

Variant summary

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

The ENST00000716354.1(ENSG00000255910):​n.4575+11516G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,116 control chromosomes in the GnomAD database, including 2,781 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 0.17 (2781 hom., cov: 34)
• Consequence: ENSG00000255910 ENST00000716354.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 9 publications found

Genes affected

ENSG00000255910 (HGNC:):

LINC02398 (HGNC:53325): (long intergenic non-protein coding RNA 2398)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716354.1. 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
	LINC02398	NR_040098.1		n.409+11516G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255910	ENST00000716354.1		n.4575+11516G>A		intron	N/A
	ENSG00000255910	ENST00000716355.1		n.5561+11516G>A		intron	N/A
	ENSG00000255910	ENST00000716356.1		n.5907+11516G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26037 AN: 151998 Hom.: 2784 Cov.: 34

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.171 AC: 26047 AN: 152116 Hom.: 2781 Cov.: 34 AF XY: 0.175 AC XY: 12981 AN XY: 74350

African (AFR) AF: 0.223 AC: 9239 AN: 41502

American (AMR) AF: 0.143 AC: 2178 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 460 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2731 AN: 5176

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4816

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10558

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8333 AN: 68006

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.145 Hom.: 3350

Bravo AF: 0.176

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11045000; hg19: chr12-20184146;