rs5755393

Variant names:

• chr22-34881047-A-G
• rs5755393
• ENST00000665218.1:n.157+3094T>C

Variant summary

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

The ENST00000665218.1(LINC02885):​n.157+3094T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,174 control chromosomes in the GnomAD database, including 31,292 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 0.62 (31292 hom., cov: 32)
• Consequence: LINC02885 ENST00000665218.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 3 publications found

Genes affected

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

LOC124905109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.460+16789T>C		intron_variant	Intron 3 of 4
LOC124905109	XR_007068083.1	n.85+3094T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000665218.1	n.157+3094T>C		intron_variant	Intron 2 of 2
LINC02885	ENST00000668433.1	n.343+21576T>C		intron_variant	Intron 3 of 3
LINC02885	ENST00000700833.2	n.319+3094T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94259 AN: 152056 Hom.: 31251 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.620 AC: 94338 AN: 152174 Hom.: 31292 Cov.: 32 AF XY: 0.612 AC XY: 45486 AN XY: 74382

African (AFR) AF: 0.882 AC: 36631 AN: 41542

American (AMR) AF: 0.541 AC: 8277 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2425 AN: 5162

South Asian (SAS) AF: 0.504 AC: 2425 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4360 AN: 10578

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36183 AN: 67998

Other (OTH) AF: 0.589 AC: 1245 AN: 2114

Alfa AF: 0.589 Hom.: 4854

Bravo AF: 0.641

Asia WGS AF: 0.461 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs5755393; hg19: chr22-35277037;