rs1457595

chr12-102591927-G-T

Variant summary

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

The XR_007063427.1(LINC02456):n.34903-98179G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0126 in 152,296 control chromosomes in the GnomAD database, including 64 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 0.013 (64 hom., cov: 33)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34903-98179G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1917 AN: 152178 Hom.: 64 Cov.: 33

Gnomad AFR AF: 0.00140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0144

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00182

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0126 AC: 1912 AN: 152296 Hom.: 64 Cov.: 33 AF XY: 0.0167 AC XY: 1243 AN XY: 74464

Gnomad4 AFR AF: 0.00140

Gnomad4 AMR AF: 0.0144

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0504

Gnomad4 FIN AF: 0.0662

Gnomad4 NFE AF: 0.00182

Gnomad4 OTH AF: 0.00994

Alfa AF: 0.00277 Hom.: 7

Bravo AF: 0.00886

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457595; hg19: chr12-102985705;