rs35747

Positions:

• chr12-102518780-G-A

Variant summary

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

The XR_007063427.1(LINC02456):​n.34902+34892G>A 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 0.705 in 152,018 control chromosomes in the GnomAD database, including 39,961 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 0.70 (39961 hom., cov: 31)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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 (NFE) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34902+34892G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107084 AN: 151900 Hom.: 39962 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.705 AC: 107109 AN: 152018 Hom.: 39961 Cov.: 31 AF XY: 0.706 AC XY: 52458 AN XY: 74310

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.725

Alfa AF: 0.814 Hom.: 81718

Bravo AF: 0.688

Asia WGS AF: 0.689 AC: 2394 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	0.37
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35747; hg19: chr12-102912558;