8-13902910-T-G

Variant names:

• chr8-13902910-T-G
• rs10888075

Variant summary

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

The variant allele was found at a frequency of 0.763 in 151,976 control chromosomes in the GnomAD database, including 45,394 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 0.76 (45394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 2 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115913 AN: 151858 Hom.: 45366 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.763 AC: 115986 AN: 151976 Hom.: 45394 Cov.: 31 AF XY: 0.761 AC XY: 56517 AN XY: 74280

African (AFR) AF: 0.583 AC: 24148 AN: 41430

American (AMR) AF: 0.809 AC: 12357 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2737 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3336 AN: 5142

South Asian (SAS) AF: 0.785 AC: 3783 AN: 4822

European-Finnish (FIN) AF: 0.840 AC: 8875 AN: 10566

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58164 AN: 67952

Other (OTH) AF: 0.760 AC: 1606 AN: 2114

Alfa AF: 0.832 Hom.: 79378

Bravo AF: 0.752

Asia WGS AF: 0.701 AC: 2436 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	4.2
DANN	Benign	0.41
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs10888075; hg19: chr8-13760419;