10-26607503-G-T

Variant names:

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

Variant summary

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

The ENST00000751485.1(ENSG00000290423):​n.60+24653G>T 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: ENSG00000290423 ENST00000751485.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751485.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03028	ENST00000637960.1	TSL:6	n.601+880C>A		intron	N/A
	ENSG00000290423	ENST00000751485.1		n.60+24653G>T		intron	N/A

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

African (AFR) AF: 0.0840 AC: 3484 AN: 41454

American (AMR) AF: 0.0802 AC: 1225 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0776 AC: 269 AN: 3468

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5178

South Asian (SAS) AF: 0.0828 AC: 399 AN: 4816

European-Finnish (FIN) AF: 0.0952 AC: 1007 AN: 10576

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5074 AN: 68004

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0713 Hom.: 882

Bravo AF: 0.0759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.080
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs787025; hg19: chr10-26896432;