12-17509301-A-T

Variant names:

• chr12-17509301-A-T
• rs1706631
• ENST00000669683.1:n.965+4249A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669683.1(ENSG00000256389):​n.965+4249A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,892 control chromosomes in the GnomAD database, including 17,871 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 0.48 (17871 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000256389 ENST00000669683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

ENSG00000256389 (HGNC:):

LINC02378 (HGNC:53301): (long intergenic non-protein coding RNA 2378)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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
ENSG00000256389	ENST00000669683.1	n.965+4249A>T		intron_variant	Intron 2 of 2
LINC02378	ENST00000540399.1	n.*52T>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72730 AN: 151774 Hom.: 17836 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.479 AC: 72820 AN: 151892 Hom.: 17871 Cov.: 32 AF XY: 0.484 AC XY: 35956 AN XY: 74248

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.480

Alfa AF: 0.341 Hom.: 993

Bravo AF: 0.493

Asia WGS AF: 0.665 AC: 2312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1706631; hg19: chr12-17662235;