8-25729264-T-C

Variant names:

• chr8-25729264-T-C
• rs1425727
• XR_001745849.2:n.238+98895T>C

Variant summary

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

The XR_001745849.2(LOC107986933):​n.238+98895T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,008 control chromosomes in the GnomAD database, including 56,251 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 0.86 (56251 hom., cov: 31)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 publications found

Genes affected

LOC107986933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130526 AN: 151888 Hom.: 56210 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.859 AC: 130620 AN: 152008 Hom.: 56251 Cov.: 31 AF XY: 0.859 AC XY: 63854 AN XY: 74318

African (AFR) AF: 0.880 AC: 36492 AN: 41464

American (AMR) AF: 0.806 AC: 12291 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2964 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4870 AN: 5170

South Asian (SAS) AF: 0.871 AC: 4207 AN: 4828

European-Finnish (FIN) AF: 0.838 AC: 8821 AN: 10526

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58230 AN: 67976

Other (OTH) AF: 0.842 AC: 1778 AN: 2112

Alfa AF: 0.858 Hom.: 23804

Bravo AF: 0.854

Asia WGS AF: 0.895 AC: 3101 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.69
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1425727; hg19: chr8-25586780;