rs11577023

Positions:

• chr1-221888631-T-C

Variant summary

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

The XR_007066885.1(LOC124904517):​n.331-27447T>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 0.273 in 152,200 control chromosomes in the GnomAD database, including 6,142 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 (6142 hom., cov: 33)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.331-27447T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-4743A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41476 AN: 152082 Hom.: 6142 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.273 AC: 41485 AN: 152200 Hom.: 6142 Cov.: 33 AF XY: 0.270 AC XY: 20123 AN XY: 74432

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.288

Alfa AF: 0.300 Hom.: 4213

Bravo AF: 0.260

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.0070
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11577023; hg19: chr1-222061973;