rs4923705

Positions:

• chr15-36001404-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000650498.1(ENSG00000259639):​n.200-26635C>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 0.673 in 152,074 control chromosomes in the GnomAD database, including 35,569 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 0.67 (35569 hom., cov: 32)
• Consequence: ENST00000650498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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
	ENST00000650498.1	n.200-26635C>T		intron_variant, non_coding_transcript_variant
LINC02853	ENST00000668741.1	n.462+25389G>A		intron_variant, non_coding_transcript_variant
	ENST00000561394.1	n.200-26635C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102291 AN: 151954 Hom.: 35573 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.673 AC: 102313 AN: 152074 Hom.: 35569 Cov.: 32 AF XY: 0.678 AC XY: 50370 AN XY: 74322

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.678

Alfa AF: 0.739 Hom.: 83751

Bravo AF: 0.638

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	20
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4923705; hg19: chr15-36293605;