rs54211

Variant names:

• chr22-39291479-A-G
• rs54211

Your query was ambiguous. Multiple possible variants found:

• chr22-39291479-A-G
• chr22-39291479-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 0.905 in 152,316 control chromosomes in the GnomAD database, including 62,441 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 0.90 (62441 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.905 AC: 137739 AN: 152198 Hom.: 62411 Cov.: 34

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.905 AC: 137820 AN: 152316 Hom.: 62441 Cov.: 34 AF XY: 0.904 AC XY: 67325 AN XY: 74464

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.913

Alfa AF: 0.892 Hom.: 132614

Bravo AF: 0.913

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs54211; hg19: chr22-39687484;