15-35972646-A-C

Variant names:

• chr15-35972646-A-C
• rs1510385
• ENST00000560886.5:n.59+2065T>G

Variant summary

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

The ENST00000560886.5(ENSG00000259639):​n.59+2065T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,846 control chromosomes in the GnomAD database, including 17,052 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 0.47 (17052 hom., cov: 31)
• Consequence: ENSG00000259639 ENST00000560886.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 2 publications found

Genes affected

ENSG00000259639 (HGNC:):

LINC02853 (HGNC:54390): (long intergenic non-protein coding RNA 2853)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560886.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259639	ENST00000560886.5	TSL:5	n.59+2065T>G		intron	N/A
	ENSG00000259639	ENST00000561394.2	TSL:3	n.259-1846T>G		intron	N/A
	ENSG00000259639	ENST00000650498.1		n.258+2065T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71679 AN: 151728 Hom.: 17038 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.472 AC: 71746 AN: 151846 Hom.: 17052 Cov.: 31 AF XY: 0.474 AC XY: 35181 AN XY: 74194

African (AFR) AF: 0.429 AC: 17769 AN: 41416

American (AMR) AF: 0.577 AC: 8800 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2453 AN: 5124

South Asian (SAS) AF: 0.502 AC: 2411 AN: 4802

European-Finnish (FIN) AF: 0.441 AC: 4667 AN: 10572

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32040 AN: 67906

Other (OTH) AF: 0.483 AC: 1016 AN: 2102

Alfa AF: 0.471 Hom.: 26598

Bravo AF: 0.482

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1510385; hg19: chr15-36264847;