10-22516023-G-C

Variant names:

• chr10-22516023-G-C
• rs1536332

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 0.209 in 151,782 control chromosomes in the GnomAD database, including 3,520 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 0.21 (3520 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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: 0.209 AC: 31704 AN: 151664 Hom.: 3522 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.209 AC: 31729 AN: 151782 Hom.: 3520 Cov.: 31 AF XY: 0.205 AC XY: 15231 AN XY: 74154

African (AFR) AF: 0.156 AC: 6449 AN: 41368

American (AMR) AF: 0.146 AC: 2223 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3464

East Asian (EAS) AF: 0.337 AC: 1736 AN: 5148

South Asian (SAS) AF: 0.167 AC: 801 AN: 4794

European-Finnish (FIN) AF: 0.216 AC: 2271 AN: 10532

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16490 AN: 67904

Other (OTH) AF: 0.195 AC: 412 AN: 2108

Alfa AF: 0.216 Hom.: 458

Bravo AF: 0.207

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.84
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1536332; hg19: chr10-22804952;