rs10823406

chr10-69552267-G-Achr10-69552267-G-C

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 0.196 in 152,076 control chromosomes in the GnomAD database, including 3,605 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 0.20 (3605 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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 = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29830 AN: 151958 Hom.: 3606 Cov.: 31

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.196 AC: 29831 AN: 152076 Hom.: 3605 Cov.: 31 AF XY: 0.194 AC XY: 14440 AN XY: 74322

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.177

Alfa AF: 0.243 Hom.: 9874

Bravo AF: 0.179

Asia WGS AF: 0.169 AC: 590 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	0.16
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10823406; hg19: chr10-71312023;