rs5755393

chr22-34881047-A-G

Variant summary

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

The NR_138042.1(LINC02885):n.460+16789T>C 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 0.62 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 NR_138042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

Genes affected

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

LOC124905109 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02885	NR_138042.1	n.460+16789T>C		intron_variant, non_coding_transcript_variant
LOC124905109	XR_007068083.1	n.85+3094T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02885	ENST00000668433.1	n.343+21576T>C		intron_variant, non_coding_transcript_variant
LINC02885	ENST00000665218.1	n.157+3094T>C		intron_variant, non_coding_transcript_variant
LINC02885	ENST00000700833.1	n.261+3094T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.589

Alfa AF: 0.581 Hom.: 4553

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5755393; hg19: chr22-35277037;