rs10774624

chr12-111395984-G-Achr12-111395984-G-C

Variant summary

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

The ENST00000552663.2(LINC02356):n.163-7154G>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 0.675 in 152,098 control chromosomes in the GnomAD database, including 37,609 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 0.68 (37609 hom., cov: 32)
• Consequence: LINC02356 ENST00000552663.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

LINC02356 (HGNC:53278): (long intergenic non-protein coding RNA 2356)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02356	ENST00000552663.2	n.163-7154G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102578 AN: 151980 Hom.: 37534 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.675 AC: 102716 AN: 152098 Hom.: 37609 Cov.: 32 AF XY: 0.687 AC XY: 51074 AN XY: 74348

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.656

Alfa AF: 0.605 Hom.: 3675

Bravo AF: 0.689

Asia WGS AF: 0.942 AC: 3273 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	2.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10774624; hg19: chr12-111833788;