rs16966460

Variant names:

• chr15-38219782-C-G
• rs16966460
• ENST00000561320.5:n.222+4469G>C

Your query was ambiguous. Multiple possible variants found:

• chr15-38219782-C-G
• chr15-38219782-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561320.5(LINC02895):​n.222+4469G>C variant causes a intron 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 ENST00000561320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 7 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=-0.85).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02895	ENST00000561320.5	n.222+4469G>C		intron_variant	Intron 2 of 3	1
LINC02895	ENST00000561161.2	n.254+4469G>C		intron_variant	Intron 2 of 2	2
LINC02895	ENST00000671149.1	n.233+4469G>C		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0620 AC: 2575 AN: 41508

American (AMR) AF: 0.159 AC: 2429 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.135 AC: 698 AN: 5176

South Asian (SAS) AF: 0.144 AC: 694 AN: 4820

European-Finnish (FIN) AF: 0.0493 AC: 521 AN: 10578

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7422 AN: 67976

Other (OTH) AF: 0.108 AC: 228 AN: 2106

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
PhyloP100		-0.073
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16966460; hg19: chr15-38511983;