15-38142690-A-G

Variant names:

• chr15-38142690-A-G
• rs10468092
• ENST00000561320.5:n.317+59T>C

Variant summary

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

The ENST00000561161.2(LINC02895):​n.408T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,844 control chromosomes in the GnomAD database, including 67,437 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 0.94 (67195 hom., cov: 33)
  • Exomes 𝑓: 0.94 (242 hom.)
• Consequence: LINC02895 ENST00000561161.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561161.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02895	ENST00000561320.5	TSL:1	n.317+59T>C		intron	N/A
	LINC02895	ENST00000561161.2	TSL:2	n.408T>C		non_coding_transcript_exon	Exon 3 of 3
	LINC02895	ENST00000728143.1		n.249-55246T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142935 AN: 152174 Hom.: 67141 Cov.: 33

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.953

GnomAD4 exome AF: 0.937 AC: 517 AN: 552 Hom.: 242 Cov.: 0 AF XY: 0.935 AC XY: 402 AN XY: 430

African (AFR) AF: 1.00 AC: 12 AN: 12

American (AMR) AF: 1.00 AC: 6 AN: 6

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AF: 1.00 AC: 20 AN: 20

South Asian (SAS) AF: 1.00 AC: 14 AN: 14

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AF: 0.833 AC: 5 AN: 6

European-Non Finnish (NFE) AF: 0.929 AC: 429 AN: 462

Other (OTH) AF: 0.958 AC: 23 AN: 24

GnomAD4 genome AF: 0.939 AC: 143048 AN: 152292 Hom.: 67195 Cov.: 33 AF XY: 0.940 AC XY: 69981 AN XY: 74454

African (AFR) AF: 0.935 AC: 38880 AN: 41566

American (AMR) AF: 0.951 AC: 14569 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3328 AN: 3472

East Asian (EAS) AF: 0.990 AC: 5115 AN: 5166

South Asian (SAS) AF: 0.926 AC: 4463 AN: 4820

European-Finnish (FIN) AF: 0.927 AC: 9838 AN: 10614

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63714 AN: 68022

Other (OTH) AF: 0.954 AC: 2016 AN: 2114

Alfa AF: 0.939 Hom.: 7643

Bravo AF: 0.943

Asia WGS AF: 0.966 AC: 3360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.14
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10468092; hg19: chr15-38434891;