rs186037

Variant names:

• chr1-22625893-A-G
• rs186037

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 0.197 in 152,142 control chromosomes in the GnomAD database, including 3,575 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 0.20 (3575 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.197 AC: 29912 AN: 152024 Hom.: 3556 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.197 AC: 29982 AN: 152142 Hom.: 3575 Cov.: 33 AF XY: 0.200 AC XY: 14850 AN XY: 74376

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.173

Alfa AF: 0.143 Hom.: 2473

Bravo AF: 0.202

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs186037; hg19: chr1-22952386;