10-86368524-A-G

Position:

• chr10-86368524-A-G

Variant summary

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

The variant allele was found at a frequency of 0.603 in 151,914 control chromosomes in the GnomAD database, including 29,537 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 0.60 (29537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91511 AN: 151796 Hom.: 29501 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.603 AC: 91591 AN: 151914 Hom.: 29537 Cov.: 32 AF XY: 0.601 AC XY: 44601 AN XY: 74230

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.545

Alfa AF: 0.530 Hom.: 29387

Bravo AF: 0.594

Asia WGS AF: 0.729 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814614; hg19: chr10-88128281;