rs725033

Variant names:

• chr1-218470598-C-T
• rs725033
• ENST00000443836.6:n.162+7005C>T

Variant summary

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

The ENST00000443836.6(LINC02869):​n.162+7005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,108 control chromosomes in the GnomAD database, including 4,780 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 0.22 (4780 hom., cov: 33)
• Consequence: LINC02869 ENST00000443836.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 5 publications found

Genes affected

LINC02869 (HGNC:32045): (long intergenic non-protein coding RNA 2869)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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
LINC02869	ENST00000443836.6	n.162+7005C>T		intron_variant	Intron 1 of 3	2
LINC02869	ENST00000663551.1	n.87+11247C>T		intron_variant	Intron 1 of 2
LINC02869	ENST00000746055.1	n.162+7005C>T		intron_variant	Intron 1 of 2
LINC02869	ENST00000746056.1	n.117+7005C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33596 AN: 151990 Hom.: 4766 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.221 AC: 33644 AN: 152108 Hom.: 4780 Cov.: 33 AF XY: 0.223 AC XY: 16597 AN XY: 74368

African (AFR) AF: 0.392 AC: 16238 AN: 41464

American (AMR) AF: 0.213 AC: 3247 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1725 AN: 5164

South Asian (SAS) AF: 0.261 AC: 1261 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1741 AN: 10588

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8458 AN: 68010

Other (OTH) AF: 0.207 AC: 437 AN: 2112

Alfa AF: 0.155 Hom.: 9839

Bravo AF: 0.229

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.34
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs725033; hg19: chr1-218643940;