rs10823406

Variant names:

• chr10-69552267-G-A
• rs10823406

Your query was ambiguous. Multiple possible variants found:

• chr10-69552267-G-A
• chr10-69552267-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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 = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0522 AC: 2168 AN: 41534

American (AMR) AF: 0.211 AC: 3226 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.115 AC: 593 AN: 5170

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4814

European-Finnish (FIN) AF: 0.287 AC: 3032 AN: 10554

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18388 AN: 67950

Other (OTH) AF: 0.177 AC: 374 AN: 2108

Alfa AF: 0.235 Hom.: 14731

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs10823406; hg19: chr10-71312023;