12-69434901-G-A

Variant names:

• chr12-69434901-G-A
• rs11177669
• ENST00000776073.1:n.372+10774G>A

Variant summary

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

The ENST00000776073.1(LINC02373):​n.372+10774G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,080 control chromosomes in the GnomAD database, including 5,911 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 0.28 (5911 hom., cov: 32)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 18 publications found

Genes affected

LINC02373 (HGNC:53295): (long intergenic non-protein coding RNA 2373)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776073.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02373	ENST00000776073.1		n.372+10774G>A		intron	N/A
	LINC02373	ENST00000776074.1		n.176+3188G>A		intron	N/A
	LINC02373	ENST00000776075.1		n.155+3188G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42061 AN: 151962 Hom.: 5890 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.277 AC: 42137 AN: 152080 Hom.: 5911 Cov.: 32 AF XY: 0.277 AC XY: 20568 AN XY: 74338

African (AFR) AF: 0.310 AC: 12839 AN: 41446

American (AMR) AF: 0.260 AC: 3979 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1416 AN: 5172

South Asian (SAS) AF: 0.350 AC: 1689 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2698 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17710 AN: 67992

Other (OTH) AF: 0.272 AC: 574 AN: 2112

Alfa AF: 0.264 Hom.: 16817

Bravo AF: 0.276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs11177669; hg19: chr12-69828681;