10-26621797-C-T

Variant names:

• chr10-26621797-C-T
• rs9665670
• ENST00000637960.1:n.270+272G>A

Variant summary

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

The ENST00000637960.1(LINC03028):​n.270+272G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,058 control chromosomes in the GnomAD database, including 34,943 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 0.67 (34943 hom., cov: 32)
• Consequence: LINC03028 ENST00000637960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 1 publications found

Genes affected

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

ENSG00000290423 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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.270+272G>A		intron_variant	Intron 1 of 7	6
ENSG00000290423	ENST00000751485.1	n.61-27594C>T		intron_variant	Intron 1 of 3
ENSG00000297927	ENST00000751858.1	n.192-8650G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101825 AN: 151940 Hom.: 34892 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.670 AC: 101934 AN: 152058 Hom.: 34943 Cov.: 32 AF XY: 0.676 AC XY: 50233 AN XY: 74318

African (AFR) AF: 0.787 AC: 32602 AN: 41446

American (AMR) AF: 0.712 AC: 10894 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3468

East Asian (EAS) AF: 0.854 AC: 4425 AN: 5182

South Asian (SAS) AF: 0.651 AC: 3138 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6931 AN: 10554

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39554 AN: 67974

Other (OTH) AF: 0.666 AC: 1407 AN: 2112

Alfa AF: 0.649 Hom.: 4794

Bravo AF: 0.679

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.42
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs9665670; hg19: chr10-26910726;