rs16966389

Positions:

• chr15-38172673-G-A
• chr15-38172673-G-C

Variant summary

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

The ENST00000561161.2(LINC02895):​n.255-29830C>T 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 0.041 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 ENST00000561161.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02895	ENST00000561161.2	n.255-29830C>T		intron_variant, non_coding_transcript_variant		2
LINC02895	ENST00000561320.5	n.223-29830C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.0908

Gnomad4 FIN AF: 0.0118

Gnomad4 NFE AF: 0.00243

Gnomad4 OTH AF: 0.0389

Alfa AF: 0.0197 Hom.: 35

Bravo AF: 0.0496

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16966389; hg19: chr15-38464874;