rs4923705

Variant names:

• chr15-36001404-G-A
• rs4923705
• ENST00000820118.1:n.322C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000820118.1(ENSG00000259639):​n.322C>T 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 0.673 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: ENSG00000259639 ENST00000820118.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 18 publications found

Genes affected

ENSG00000259639 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259639	ENST00000820118.1	n.322C>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000259639	ENST00000561394.2	n.200-26635C>T		intron_variant	Intron 3 of 4	3
ENSG00000259639	ENST00000650498.1	n.200-26635C>T		intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.509 AC: 21096 AN: 41484

American (AMR) AF: 0.577 AC: 8800 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2333 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3244 AN: 5156

South Asian (SAS) AF: 0.755 AC: 3636 AN: 4818

European-Finnish (FIN) AF: 0.866 AC: 9175 AN: 10600

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51629 AN: 67962

Other (OTH) AF: 0.678 AC: 1435 AN: 2116

Alfa AF: 0.721 Hom.: 131536

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
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4923705; hg19: chr15-36293605;