rs4010558

Variant names:

• chr22-16416036-G-A
• rs4010558

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 0.249 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.250 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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.283

Alfa AF: 0.259 Hom.: 682

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4010558; hg19: chr22-16896762;