rs11118883

Positions:

• chr1-221887680-G-A
• chr1-221887680-G-C
• chr1-221887680-G-T

Variant summary

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

The XR_007066885.1(LOC124904517):​n.331-28398G>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 0.27 in 151,788 control chromosomes in the GnomAD database, including 5,982 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 (5982 hom., cov: 32)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.331-28398G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-3792C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40989 AN: 151670 Hom.: 5980 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.270 AC: 40995 AN: 151788 Hom.: 5982 Cov.: 32 AF XY: 0.268 AC XY: 19864 AN XY: 74164

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.280

Alfa AF: 0.289 Hom.: 10744

Bravo AF: 0.256

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11118883; hg19: chr1-222061022;