chr15-38172673-G-A

Variant names:

• chr15-38172673-G-A
• rs16966389
• ENST00000561320.5:n.223-29830C>T

Variant summary

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

The ENST00000561320.5(LINC02895):​n.223-29830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 152,126 control chromosomes in the GnomAD database, including 477 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 0.041 (477 hom., cov: 32)
• Consequence: LINC02895 ENST00000561320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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.223-29830C>T		intron	N/A
	LINC02895	ENST00000561161.2	TSL:2	n.255-29830C>T		intron	N/A
	LINC02895	ENST00000728143.1		n.248+51578C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0408 AC: 6203 AN: 152008 Hom.: 474 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00243

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0410 AC: 6230 AN: 152126 Hom.: 477 Cov.: 32 AF XY: 0.0448 AC XY: 3332 AN XY: 74360

African (AFR) AF: 0.0493 AC: 2047 AN: 41522

American (AMR) AF: 0.110 AC: 1675 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1691 AN: 5140

South Asian (SAS) AF: 0.0908 AC: 437 AN: 4812

European-Finnish (FIN) AF: 0.0118 AC: 125 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00243 AC: 165 AN: 67992

Other (OTH) AF: 0.0389 AC: 82 AN: 2108

Alfa AF: 0.0416 Hom.: 296

Bravo AF: 0.0496

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.93
DANN	Benign	0.38
PhyloP100		0.014

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: rs16966389;

hg19: chr15-38464874;