10-26607503-G-T

Variant names:

• chr10-26607503-G-T
• rs787025
• ENST00000637960.1:n.601+880C>A

Variant summary

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

The ENST00000637960.1(LINC03028):​n.601+880C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,086 control chromosomes in the GnomAD database, including 503 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 0.078 (503 hom., cov: 32)
• Consequence: LINC03028 ENST00000637960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

Genes affected

LINC03028 (HGNC:56168): (long intergenic non-protein coding RNA 3028)

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 (AFR) allele frequency at 95% confidence interval = 0.0817 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
LINC03028	ENST00000637960.1	n.601+880C>A		intron_variant	Intron 4 of 7	6

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11826 AN: 151968 Hom.: 505 Cov.: 32

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.0952

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0985

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

GnomAD4 genome AF: 0.0778 AC: 11832 AN: 152086 Hom.: 503 Cov.: 32 AF XY: 0.0789 AC XY: 5865 AN XY: 74364

Gnomad4 AFR AF: 0.0840

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.0776

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.0952

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0666 Hom.: 215

Bravo AF: 0.0759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.080

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs787025; hg19: chr10-26896432;