10-25898748-T-G

Variant names:

• chr10-25898748-T-G
• rs7086207
• ENST00000744999.1:n.378-5329A>C

Variant summary

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

The ENST00000744999.1(ENSG00000226304):​n.378-5329A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,796 control chromosomes in the GnomAD database, including 12,604 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 0.41 (12604 hom., cov: 30)
• Consequence: ENSG00000226304 ENST00000744999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

Genes affected

ENSG00000226304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744999.1. 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
	ENSG00000226304	ENST00000744999.1		n.378-5329A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61608 AN: 151680 Hom.: 12601 Cov.: 30

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.406 AC: 61634 AN: 151796 Hom.: 12604 Cov.: 30 AF XY: 0.405 AC XY: 29992 AN XY: 74140

African (AFR) AF: 0.426 AC: 17654 AN: 41400

American (AMR) AF: 0.305 AC: 4649 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1501 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1458 AN: 5158

South Asian (SAS) AF: 0.445 AC: 2138 AN: 4806

European-Finnish (FIN) AF: 0.449 AC: 4718 AN: 10508

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28278 AN: 67892

Other (OTH) AF: 0.403 AC: 846 AN: 2100

Alfa AF: 0.395 Hom.: 6523

Bravo AF: 0.389

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.62
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7086207;

hg19: chr10-26187677;