rs11723530

chr4-169959732-G-A

Variant summary

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

The NR_037878.1(LINC02275):n.87+16084C>T 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 0.398 in 151,890 control chromosomes in the GnomAD database, including 13,519 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 0.40 (13519 hom., cov: 31)
• Consequence: LINC02275 NR_037878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

Genes affected

LINC02275 (HGNC:53191): (long intergenic non-protein coding RNA 2275)

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02275	NR_037878.1	n.87+16084C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02275	ENST00000508313.3	n.95+16084C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000509956.1	n.250-3403G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60366 AN: 151772 Hom.: 13509 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.398 AC: 60387 AN: 151890 Hom.: 13519 Cov.: 31 AF XY: 0.396 AC XY: 29405 AN XY: 74226

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.0486

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.407

Alfa AF: 0.480 Hom.: 36921

Bravo AF: 0.381

Asia WGS AF: 0.204 AC: 712 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	0.028
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11723530; hg19: chr4-170880883;