rs35747

Variant names:

• chr12-102518780-G-A
• rs35747
• ENST00000758464.1:n.284+4401G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-102518780-G-A
• chr12-102518780-G-C
• chr12-102518780-G-T

Variant summary

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

The ENST00000758464.1(ENSG00000298855):​n.284+4401G>A variant causes a intron 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: ENSG00000298855 ENST00000758464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 19 publications found

Genes affected

ENSG00000298855 (HGNC:):

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+34892G>A		intron_variant	Intron 11 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298855	ENST00000758464.1	n.284+4401G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.434 AC: 17965 AN: 41404

American (AMR) AF: 0.768 AC: 11737 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2646 AN: 3472

East Asian (EAS) AF: 0.657 AC: 3395 AN: 5168

South Asian (SAS) AF: 0.761 AC: 3668 AN: 4820

European-Finnish (FIN) AF: 0.792 AC: 8371 AN: 10566

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56783 AN: 67992

Other (OTH) AF: 0.725 AC: 1530 AN: 2110

Alfa AF: 0.796 Hom.: 189480

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs35747; hg19: chr12-102912558;