rs16966413

Variant names:

• chr15-38187698-A-G
• rs16966413
• ENST00000561320.5:n.222+36553T>C

Variant summary

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

The ENST00000561320.5(LINC02895):​n.222+36553T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,188 control chromosomes in the GnomAD database, including 775 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 0.088 (775 hom., cov: 32)
• Consequence: LINC02895 ENST00000561320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02895	ENST00000561320.5	n.222+36553T>C		intron_variant	Intron 2 of 3	1
LINC02895	ENST00000561161.2	n.254+36553T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13416 AN: 152070 Hom.: 775 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0987

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0882 AC: 13420 AN: 152188 Hom.: 775 Cov.: 32 AF XY: 0.0895 AC XY: 6659 AN XY: 74422

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.0604

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0983 Hom.: 162

Bravo AF: 0.0929

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16966413; hg19: chr15-38479899;