rs225537

Positions:

• chr12-126000924-A-G

Variant summary

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

The NR_183612.1(LINC02826):​n.696+13695A>G 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 0.362 in 151,946 control chromosomes in the GnomAD database, including 11,445 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 0.36 (11445 hom., cov: 32)
• Consequence: LINC02826 NR_183612.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775

Genes affected

LINC02826 (HGNC:54357): (long intergenic non-protein coding RNA 2826)

LOC105370058 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02826	NR_183612.1	n.696+13695A>G		intron_variant, non_coding_transcript_variant
LOC105370058	XR_945503.2	n.107+965T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02826	ENST00000642407.1	n.511+13695A>G		intron_variant, non_coding_transcript_variant
LINC02826	ENST00000660252.1	n.2768-29A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54971 AN: 151828 Hom.: 11421 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.362 AC: 55035 AN: 151946 Hom.: 11445 Cov.: 32 AF XY: 0.360 AC XY: 26739 AN XY: 74240

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.343

Alfa AF: 0.329 Hom.: 1137

Bravo AF: 0.369

Asia WGS AF: 0.245 AC: 853 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	1.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225537; hg19: chr12-126485470;