rs10088262

Variant names:

• chr8-123753462-A-G
• rs10088262
• XR_928607.4:n.82-11321A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-123753462-A-G
• chr8-123753462-A-T

Variant summary

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

The XR_928607.4(LOC105375739):​n.82-11321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,958 control chromosomes in the GnomAD database, including 27,424 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 0.56 (27424 hom., cov: 31)
• Consequence: LOC105375739 XR_928607.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 20 publications found

Genes affected

LOC105375739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 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: 0.565 AC: 85730 AN: 151840 Hom.: 27427 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.564 AC: 85738 AN: 151958 Hom.: 27424 Cov.: 31 AF XY: 0.565 AC XY: 41991 AN XY: 74266

African (AFR) AF: 0.237 AC: 9822 AN: 41428

American (AMR) AF: 0.592 AC: 9039 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3468

East Asian (EAS) AF: 0.662 AC: 3416 AN: 5158

South Asian (SAS) AF: 0.679 AC: 3271 AN: 4816

European-Finnish (FIN) AF: 0.683 AC: 7219 AN: 10566

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48114 AN: 67938

Other (OTH) AF: 0.607 AC: 1278 AN: 2104

Alfa AF: 0.673 Hom.: 166790

Bravo AF: 0.545

Asia WGS AF: 0.632 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10088262; hg19: chr8-124765702;