chr12-127329196-G-A

Variant names:

• chr12-127329196-G-A
• rs10744304
• ENST00000545739.2:n.228-4391C>T

Variant summary

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

The ENST00000545739.2(LINC02375):​n.228-4391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,068 control chromosomes in the GnomAD database, including 21,830 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 0.51 (21830 hom., cov: 32)
• Consequence: LINC02375 ENST00000545739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 4 publications found

Genes affected

LINC02375 (HGNC:53297): (long intergenic non-protein coding RNA 2375)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02375	NR_110057.1	n.202-4391C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02375	ENST00000545739.2	n.228-4391C>T		intron_variant	Intron 2 of 2	1
LINC02375	ENST00000657634.2	n.294-4391C>T		intron_variant	Intron 2 of 2
LINC02375	ENST00000670647.2	n.282-4391C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77327 AN: 151948 Hom.: 21825 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.509 AC: 77340 AN: 152068 Hom.: 21830 Cov.: 32 AF XY: 0.513 AC XY: 38137 AN XY: 74362

African (AFR) AF: 0.243 AC: 10102 AN: 41498

American (AMR) AF: 0.551 AC: 8422 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2341 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2934 AN: 5142

South Asian (SAS) AF: 0.638 AC: 3077 AN: 4826

European-Finnish (FIN) AF: 0.621 AC: 6567 AN: 10570

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42018 AN: 67966

Other (OTH) AF: 0.565 AC: 1191 AN: 2108

Alfa AF: 0.543 Hom.: 18984

Bravo AF: 0.490

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.052
DANN	Benign	0.33
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs10744304; hg19: chr12-127813741;