12-69433878-G-T

Variant names:

• chr12-69433878-G-T
• rs10748128
• ENST00000776073.1:n.372+9751G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000776073.1(LINC02373):​n.372+9751G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,010 control chromosomes in the GnomAD database, including 14,555 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 0.42 (14555 hom., cov: 32)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 60 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02373	ENST00000776073.1	n.372+9751G>T		intron_variant	Intron 3 of 4
LINC02373	ENST00000776074.1	n.176+2165G>T		intron_variant	Intron 1 of 3
LINC02373	ENST00000776075.1	n.155+2165G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64304 AN: 151892 Hom.: 14525 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.424 AC: 64393 AN: 152010 Hom.: 14555 Cov.: 32 AF XY: 0.424 AC XY: 31513 AN XY: 74300

African (AFR) AF: 0.563 AC: 23361 AN: 41458

American (AMR) AF: 0.367 AC: 5601 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3360 AN: 5148

South Asian (SAS) AF: 0.517 AC: 2490 AN: 4820

European-Finnish (FIN) AF: 0.346 AC: 3662 AN: 10574

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23419 AN: 67950

Other (OTH) AF: 0.398 AC: 840 AN: 2110

Alfa AF: 0.367 Hom.: 47431

Bravo AF: 0.426

Asia WGS AF: 0.583 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10748128; hg19: chr12-69827658;