10-84992589-A-G

Variant names:

• chr10-84992589-A-G
• rs10788392
• XR_001747520.2:n.71+390T>C

Variant summary

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

The XR_001747520.2(LOC107984249):​n.71+390T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,958 control chromosomes in the GnomAD database, including 32,963 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 0.65 (32963 hom., cov: 31)
• Consequence: LOC107984249 XR_001747520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 3 publications found

Genes affected

LOC107984249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.651 AC: 98795 AN: 151840 Hom.: 32911 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.651 AC: 98903 AN: 151958 Hom.: 32963 Cov.: 31 AF XY: 0.648 AC XY: 48130 AN XY: 74260

African (AFR) AF: 0.795 AC: 32969 AN: 41462

American (AMR) AF: 0.697 AC: 10644 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2090 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3186 AN: 5128

South Asian (SAS) AF: 0.634 AC: 3047 AN: 4804

European-Finnish (FIN) AF: 0.505 AC: 5342 AN: 10580

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39571 AN: 67932

Other (OTH) AF: 0.659 AC: 1391 AN: 2110

Alfa AF: 0.605 Hom.: 15517

Bravo AF: 0.671

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.48
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10788392; hg19: chr10-86752345;