rs16966460

chr15-38219782-C-Gchr15-38219782-C-T

Variant summary

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

The ENST00000561161.2(LINC02895):n.254+4469G>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 0.0997 in 152,106 control chromosomes in the GnomAD database, including 860 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 (860 hom., cov: 33)
• Consequence: LINC02895 ENST00000561161.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

LINC02895 (HGNC:55422): (long intergenic non-protein coding RNA 2895)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02895	ENST00000561161.2	n.254+4469G>C		intron_variant, non_coding_transcript_variant		2
LINC02895	ENST00000561320.5	n.222+4469G>C		intron_variant, non_coding_transcript_variant		1
LINC02895	ENST00000671149.1	n.233+4469G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0997 AC: 15159 AN: 151988 Hom.: 863 Cov.: 33

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0997 AC: 15161 AN: 152106 Hom.: 860 Cov.: 33 AF XY: 0.0995 AC XY: 7401 AN XY: 74348

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.108

Alfa AF: 0.103 Hom.: 100

Bravo AF: 0.109

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.2
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16966460; hg19: chr15-38511983;