1-221882415-G-C

Variant summary

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

The XR_007066885.1(LOC124904517):n.330+30350G>C 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 0.266 in 151,940 control chromosomes in the GnomAD database, including 6,018 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 (6018 hom., cov: 31)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.330+30350G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.417-1131C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40445 AN: 151822 Hom.: 6017 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.266 AC: 40440 AN: 151940 Hom.: 6018 Cov.: 31 AF XY: 0.264 AC XY: 19584 AN XY: 74244

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.286

Alfa AF: 0.171 Hom.: 372

Bravo AF: 0.250

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.51
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12137702; hg19: chr1-222055757;