rs10505648

Variant names:

• chr8-136144207-A-G
• rs10505648
• ENST00000502901.6:n.186-18268A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-136144207-A-G
• chr8-136144207-A-T

Variant summary

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

The ENST00000502901.6(LINC02055):​n.186-18268A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,610 control chromosomes in the GnomAD database, including 14,982 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 0.43 (14982 hom., cov: 31)
• Consequence: LINC02055 ENST00000502901.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 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
LINC02055	ENST00000502901.6	n.186-18268A>G		intron_variant	Intron 1 of 3	4
LINC02055	ENST00000523150.1	n.331-18268A>G		intron_variant	Intron 2 of 4	5
LINC02055	ENST00000648077.2	n.284-54023A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64455 AN: 151492 Hom.: 14983 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.425 AC: 64450 AN: 151610 Hom.: 14982 Cov.: 31 AF XY: 0.422 AC XY: 31284 AN XY: 74068

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.0933

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.429

Alfa AF: 0.491 Hom.: 24555

Bravo AF: 0.403

Asia WGS AF: 0.211 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505648; hg19: chr8-137156450;