chr10-88008827-G-A

Position:

• chr10-88008827-G-A

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 0.139 in 152,194 control chromosomes in the GnomAD database, including 1,813 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 0.14 (1813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

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 (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.139 AC: 21181 AN: 152076 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.139 AC: 21212 AN: 152194 Hom.: 1813 Cov.: 32 AF XY: 0.140 AC XY: 10392 AN XY: 74382

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.148

Alfa AF: 0.140 Hom.: 1338

Bravo AF: 0.147

Asia WGS AF: 0.237 AC: 825 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	5.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788575; hg19: chr10-89768584;