10-121259506-T-C

Variant names:

• chr10-121259506-T-C
• rs3925042
• ENST00000718585.1:n.66+25899A>G

Variant summary

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

The ENST00000718585.1(ENSG00000293725):​n.66+25899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,056 control chromosomes in the GnomAD database, including 26,705 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 0.59 (26705 hom., cov: 32)
• Consequence: ENSG00000293725 ENST00000718585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 2 publications found

Genes affected

ENSG00000293725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718585.1. 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
	ENSG00000293725	ENST00000718585.1		n.66+25899A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89290 AN: 151938 Hom.: 26688 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.588 AC: 89340 AN: 152056 Hom.: 26705 Cov.: 32 AF XY: 0.588 AC XY: 43722 AN XY: 74320

African (AFR) AF: 0.474 AC: 19659 AN: 41456

American (AMR) AF: 0.615 AC: 9388 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2252 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3159 AN: 5170

South Asian (SAS) AF: 0.793 AC: 3819 AN: 4816

European-Finnish (FIN) AF: 0.577 AC: 6098 AN: 10574

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42972 AN: 67990

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.470 Hom.: 1614

Bravo AF: 0.583

Asia WGS AF: 0.693 AC: 2408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		0.69

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: rs3925042;

hg19: chr10-123019020;