rs1510385

Positions:

• chr15-35972646-A-C
• chr15-35972646-A-T

Variant summary

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

The ENST00000650498.1(ENSG00000259639):​n.258+2065T>G 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 0.472 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: ENST00000650498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370766	XR_001751478.1	n.246-3276A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650498.1	n.258+2065T>G		intron_variant, non_coding_transcript_variant
LINC02853	ENST00000668741.1	n.369-3276A>C		intron_variant, non_coding_transcript_variant
	ENST00000560886.5	n.59+2065T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000561394.1	n.259-1846T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.483

Alfa AF: 0.469 Hom.: 21975

Bravo AF: 0.482

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1510385; hg19: chr15-36264847;