rs12743521

chr1-221927606-G-Achr1-221927606-G-C

Variant summary

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

The NR_149057.1(LINC02257):n.162-8894C>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 0.223 in 152,040 control chromosomes in the GnomAD database, including 4,217 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 0.22 (4217 hom., cov: 31)
• Consequence: LINC02257 NR_149057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

Genes affected

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02257	NR_149057.1	n.162-8894C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000412445.1	n.165-8894C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33863 AN: 151922 Hom.: 4209 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.223 AC: 33888 AN: 152040 Hom.: 4217 Cov.: 31 AF XY: 0.223 AC XY: 16596 AN XY: 74334

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.232

Alfa AF: 0.236 Hom.: 2314

Bravo AF: 0.220

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.10
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12743521; hg19: chr1-222100948;