rs12759486

Positions:

• chr1-221893194-C-T

Variant summary

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

The XR_007066885.1(LOC124904517):​n.331-22884C>T 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 0.466 in 151,842 control chromosomes in the GnomAD database, including 17,267 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 0.47 (17267 hom., cov: 31)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LOC124904517 (HGNC:):

LINC02257 (HGNC:53159): (long intergenic non-protein coding RNA 2257)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.331-22884C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-9306G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70742 AN: 151724 Hom.: 17254 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.466 AC: 70795 AN: 151842 Hom.: 17267 Cov.: 31 AF XY: 0.462 AC XY: 34267 AN XY: 74188

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.477

Alfa AF: 0.442 Hom.: 3378

Bravo AF: 0.464

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12759486; hg19: chr1-222066536;