rs10088262

chr8-123753462-A-Gchr8-123753462-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928607.4(LOC105375739):n.82-11321A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

LOC105375739 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375739	XR_928607.4	n.82-11321A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.607

Alfa AF: 0.696 Hom.: 84447

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10088262; hg19: chr8-124765702;