rs13054085

Variant names:

• chr22-48234372-G-A
• rs13054085

Your query was ambiguous. Multiple possible variants found:

• chr22-48234372-G-A
• chr22-48234372-G-T

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 0.0571 in 152,212 control chromosomes in the GnomAD database, including 567 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 0.057 (567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.0571 AC: 8692 AN: 152094 Hom.: 570 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0571 AC: 8686 AN: 152212 Hom.: 567 Cov.: 32 AF XY: 0.0633 AC XY: 4708 AN XY: 74414

African (AFR) AF: 0.0598 AC: 2483 AN: 41522

American (AMR) AF: 0.121 AC: 1848 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.306 AC: 1584 AN: 5170

South Asian (SAS) AF: 0.104 AC: 500 AN: 4830

European-Finnish (FIN) AF: 0.0768 AC: 814 AN: 10598

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1260 AN: 68020

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0417 Hom.: 836

Bravo AF: 0.0638

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.42
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs13054085; hg19: chr22-48630184;