rs10774624

Variant names:

• chr12-111395984-G-A
• rs10774624
• ENST00000548846.2:n.269-847G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-111395984-G-A
• chr12-111395984-G-C

Variant summary

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

The ENST00000548846.2(LINC02356):​n.269-847G>A variant causes a intron 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 ENST00000548846.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 101 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02356	NR_187520.1	n.61-847G>A		intron_variant	Intron 1 of 2
LINC02356	NR_187521.1	n.163-7154G>A		intron_variant	Intron 2 of 2
LINC02356	NR_187522.1	n.163-847G>A		intron_variant	Intron 2 of 3
LINC02356	NR_187523.1	n.105+2094G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02356	ENST00000548846.2	n.269-847G>A		intron_variant	Intron 1 of 2	3
LINC02356	ENST00000552663.3	n.361-7154G>A		intron_variant	Intron 2 of 2	3
LINC02356	ENST00000722283.1	n.239-847G>A		intron_variant	Intron 2 of 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

African (AFR) AF: 0.917 AC: 38107 AN: 41538

American (AMR) AF: 0.698 AC: 10652 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5172 AN: 5186

South Asian (SAS) AF: 0.905 AC: 4368 AN: 4828

European-Finnish (FIN) AF: 0.603 AC: 6356 AN: 10548

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34868 AN: 67954

Other (OTH) AF: 0.656 AC: 1382 AN: 2106

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10774624; hg19: chr12-111833788;