rs10016872

chr4-169959225-C-T

Variant summary

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

The NR_037878.1(LINC02275):n.88-16382G>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 0.501 in 152,118 control chromosomes in the GnomAD database, including 19,438 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 0.50 (19438 hom., cov: 32)
• Consequence: LINC02275 NR_037878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02275	NR_037878.1	n.88-16382G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02275	ENST00000508313.3	n.96-16382G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000509956.1	n.250-3910C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76223 AN: 152000 Hom.: 19421 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.501 AC: 76285 AN: 152118 Hom.: 19438 Cov.: 32 AF XY: 0.497 AC XY: 36952 AN XY: 74390

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.495

Alfa AF: 0.517 Hom.: 10046

Bravo AF: 0.498

Asia WGS AF: 0.284 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.2
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10016872; hg19: chr4-170880376;