rs4010558

Variant names:

• chr22-16416036-G-A
• rs4010558

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 0.249 in 152,034 control chromosomes in the GnomAD database, including 5,448 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 0.25 (5448 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37907 AN: 151916 Hom.: 5436 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.249 AC: 37927 AN: 152034 Hom.: 5448 Cov.: 33 AF XY: 0.251 AC XY: 18622 AN XY: 74310

African (AFR) AF: 0.101 AC: 4200 AN: 41506

American (AMR) AF: 0.352 AC: 5380 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1128 AN: 3464

East Asian (EAS) AF: 0.374 AC: 1921 AN: 5142

South Asian (SAS) AF: 0.314 AC: 1512 AN: 4816

European-Finnish (FIN) AF: 0.224 AC: 2364 AN: 10576

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20521 AN: 67950

Other (OTH) AF: 0.283 AC: 596 AN: 2108

Alfa AF: 0.279 Hom.: 1885

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4010558; hg19: chr22-16896762;