15-39021201-C-G

Variant names:

• chr15-39021201-C-G
• rs1821380
• ENST00000560197.6:n.171-46966G>C

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.174-46966G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,046 control chromosomes in the GnomAD database, including 13,547 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 0.42 (13547 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000560484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 13 publications found

Genes affected

ENSG00000259345 (HGNC:):

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560484.1. 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
	LOC105370781	NR_188221.1		n.89+1877C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259345	ENST00000560197.6	TSL:5	n.171-46966G>C		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.174-46966G>C		intron	N/A
	ENSG00000259278	ENST00000560709.1	TSL:4	n.92+1877C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63803 AN: 151928 Hom.: 13536 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.420 AC: 63839 AN: 152046 Hom.: 13547 Cov.: 32 AF XY: 0.416 AC XY: 30891 AN XY: 74342

African (AFR) AF: 0.391 AC: 16230 AN: 41466

American (AMR) AF: 0.436 AC: 6658 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1978 AN: 5172

South Asian (SAS) AF: 0.353 AC: 1701 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4247 AN: 10574

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30153 AN: 67964

Other (OTH) AF: 0.436 AC: 920 AN: 2112

Alfa AF: 0.420 Hom.: 1670

Bravo AF: 0.422

Asia WGS AF: 0.391 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.18
PhyloP100		0.87

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: rs1821380;

hg19: chr15-39313402;