10-58322908-G-A

Variant names:

• chr10-58322908-G-A
• rs16912145

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 0.191 in 152,030 control chromosomes in the GnomAD database, including 4,041 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 0.19 (4041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29047 AN: 151912 Hom.: 4026 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.191 AC: 29101 AN: 152030 Hom.: 4041 Cov.: 32 AF XY: 0.192 AC XY: 14251 AN XY: 74322

African (AFR) AF: 0.391 AC: 16209 AN: 41404

American (AMR) AF: 0.154 AC: 2355 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3466

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5174

South Asian (SAS) AF: 0.179 AC: 863 AN: 4818

European-Finnish (FIN) AF: 0.0823 AC: 870 AN: 10576

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.0926 AC: 6295 AN: 68004

Other (OTH) AF: 0.173 AC: 365 AN: 2114

Alfa AF: 0.124 Hom.: 6105

Bravo AF: 0.208

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.56
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs16912145; hg19: chr10-60082668;