rs17419851

chr6-24749185-C-T

Variant summary

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

The NR_183315.1(LINC02828):n.195+37C>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 0.103 in 152,202 control chromosomes in the GnomAD database, including 956 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 0.10 (954 hom., cov: 32)
  • Exomes 𝑓: 0.14 (2 hom.)
• Consequence: LINC02828 NR_183315.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

LINC02828 (HGNC:54359): (long intergenic non-protein coding RNA 2828)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02828	NR_183315.1	n.195+37C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02828	ENST00000665572.1	n.420+37C>T		intron_variant, non_coding_transcript_variant
LINC02828	ENST00000423504.2	n.201+37C>T		intron_variant, non_coding_transcript_variant		2
LINC02828	ENST00000453179.1	n.198+37C>T		intron_variant, non_coding_transcript_variant		4
LINC02828	ENST00000668439.1	n.238-2378C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15614 AN: 152042 Hom.: 954 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.104

GnomAD4 exome AF: 0.143 AC: 6 AN: 42 Hom.: 2 Cov.: 0 AF XY: 0.176 AC XY: 6 AN XY: 34

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.103 AC: 15618 AN: 152160 Hom.: 954 Cov.: 32 AF XY: 0.102 AC XY: 7570 AN XY: 74400

Gnomad4 AFR AF: 0.0530

Gnomad4 AMR AF: 0.0813

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00657

Gnomad4 SAS AF: 0.0600

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.103

Alfa AF: 0.128 Hom.: 1771

Bravo AF: 0.0987

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.91
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17419851; hg19: chr6-24749413;