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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375739	XR_928607.4	n.82-11321A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;