chr10-25865536-G-T

Variant names:

• chr10-25865536-G-T
• rs10508706
• ENST00000744909.1:n.399+12846G>T

Variant summary

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

The ENST00000744909.1(ENSG00000297038):​n.399+12846G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,026 control chromosomes in the GnomAD database, including 8,104 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 0.32 (8104 hom., cov: 32)
• Consequence: ENSG00000297038 ENST00000744909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 1 publications found

Genes affected

ENSG00000297038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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
ENSG00000297038	ENST00000744909.1	n.399+12846G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48917 AN: 151908 Hom.: 8097 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.322 AC: 48962 AN: 152026 Hom.: 8104 Cov.: 32 AF XY: 0.316 AC XY: 23456 AN XY: 74298

African (AFR) AF: 0.323 AC: 13382 AN: 41480

American (AMR) AF: 0.312 AC: 4757 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3470

East Asian (EAS) AF: 0.0535 AC: 277 AN: 5180

South Asian (SAS) AF: 0.326 AC: 1564 AN: 4804

European-Finnish (FIN) AF: 0.280 AC: 2951 AN: 10554

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23932 AN: 67958

Other (OTH) AF: 0.324 AC: 683 AN: 2108

Alfa AF: 0.236 Hom.: 610

Bravo AF: 0.322

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10508706; hg19: chr10-26154465;