rs12726661

chr1-221894446-A-G

Variant summary

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

The XR_007066885.1(LOC124904517):n.331-21632A>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 0.268 in 145,922 control chromosomes in the GnomAD database, including 5,404 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 0.27 (5404 hom., cov: 32)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.331-21632A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-10558T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.268 AC: 39054 AN: 145812 Hom.: 5402 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00147

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.268 AC: 39062 AN: 145922 Hom.: 5404 Cov.: 32 AF XY: 0.266 AC XY: 18952 AN XY: 71294

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.00147

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.279

Alfa AF: 0.188 Hom.: 662

Asia WGS AF: 0.0950 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.7
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12726661; hg19: chr1-222067788;