rs4407

Variant names:

• chr22-48345986-A-G
• rs4407

Your query was ambiguous. Multiple possible variants found:

• chr22-48345986-A-G
• chr22-48345986-A-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 0.328 in 152,152 control chromosomes in the GnomAD database, including 9,020 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 0.33 (9020 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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: 0.328 AC: 49850 AN: 152034 Hom.: 9015 Cov.: 34

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.328 AC: 49891 AN: 152152 Hom.: 9020 Cov.: 34 AF XY: 0.331 AC XY: 24598 AN XY: 74370

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.338

Alfa AF: 0.382 Hom.: 12062

Bravo AF: 0.318

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4407; hg19: chr22-48741798;