1-221929020-C-T

Variant summary

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

The NR_149057.1(LINC02257):n.162-10308G>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 0.237 in 151,966 control chromosomes in the GnomAD database, including 4,570 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 0.24 (4570 hom., cov: 31)
• Consequence: LINC02257 NR_149057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02257	NR_149057.1	n.162-10308G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000412445.1	n.165-10308G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36032 AN: 151848 Hom.: 4560 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.237 AC: 36063 AN: 151966 Hom.: 4570 Cov.: 31 AF XY: 0.238 AC XY: 17647 AN XY: 74266

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.243

Alfa AF: 0.263 Hom.: 5583

Bravo AF: 0.236

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.73
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7544501; hg19: chr1-222102362;