rs4820425

Variant names:

• chr22-41035338-C-A
• rs4820425

Your query was ambiguous. Multiple possible variants found:

• chr22-41035338-C-A
• chr22-41035338-C-G
• chr22-41035338-C-T

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 0.256 in 151,910 control chromosomes in the GnomAD database, including 5,903 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 0.26 (5903 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.464 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: 0.256 AC: 38929 AN: 151792 Hom.: 5891 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.256 AC: 38950 AN: 151910 Hom.: 5903 Cov.: 30 AF XY: 0.265 AC XY: 19675 AN XY: 74228

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.270

Alfa AF: 0.245 Hom.: 2460

Bravo AF: 0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4820425; hg19: chr22-41431342;