rs2660664

Positions:

• chr8-136514080-G-A
• chr8-136514080-G-C

Variant summary

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

The ENST00000650445.2(LINC02055):​n.239-1345G>A 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 0.693 in 151,614 control chromosomes in the GnomAD database, including 37,297 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 0.69 (37297 hom., cov: 29)
• Consequence: LINC02055 ENST00000650445.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

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

LOC124900255 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900255	XR_007061190.1	n.75-1886G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000650445.2	n.239-1345G>A		intron_variant, non_coding_transcript_variant
LINC02055	ENST00000650470.1	n.405-1886G>A		intron_variant, non_coding_transcript_variant
LINC02055	ENST00000660691.1	n.76-1886G>A		intron_variant, non_coding_transcript_variant
LINC02055	ENST00000663951.1	n.56-1886G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105024 AN: 151492 Hom.: 37250 Cov.: 29

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.693 AC: 105127 AN: 151614 Hom.: 37297 Cov.: 29 AF XY: 0.695 AC XY: 51451 AN XY: 74054

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.687

Alfa AF: 0.635 Hom.: 14153

Bravo AF: 0.700

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2660664; hg19: chr8-137526323;