rs16966413

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561320.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02895	ENST00000561320.5	TSL:1	n.222+36553T>C		intron	N/A
	LINC02895	ENST00000561161.2	TSL:2	n.254+36553T>C		intron	N/A
	LINC02895	ENST00000728143.1		n.248+36553T>C		intron	N/A

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

African (AFR) AF: 0.0277 AC: 1151 AN: 41570

American (AMR) AF: 0.139 AC: 2120 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3470

East Asian (EAS) AF: 0.0992 AC: 505 AN: 5092

South Asian (SAS) AF: 0.178 AC: 858 AN: 4828

European-Finnish (FIN) AF: 0.0604 AC: 640 AN: 10602

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7269 AN: 68014

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.0983 Hom.: 162

Bravo AF: 0.0929

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.0
DANN	Benign	0.85
PhyloP100		-0.64

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16966413;

hg19: chr15-38479899;