rs13057866

Variant names:

• chr22-37673615-G-A
• rs13057866

Your query was ambiguous. Multiple possible variants found:

• chr22-37673615-G-A
• chr22-37673615-G-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 0.0417 in 150,876 control chromosomes in the GnomAD database, including 275 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 0.042 (275 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 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: 0.0416 AC: 6270 AN: 150764 Hom.: 275 Cov.: 31

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0417 AC: 6288 AN: 150876 Hom.: 275 Cov.: 31 AF XY: 0.0427 AC XY: 3140 AN XY: 73620

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.0611

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0268 Hom.: 23

Bravo AF: 0.0516

Asia WGS AF: 0.115 AC: 398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13057866; hg19: chr22-38069622;