rs186037

Variant names:

• chr1-22625893-A-G
• rs186037

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 0.197 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.337 AC: 13965 AN: 41492

American (AMR) AF: 0.167 AC: 2557 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3472

East Asian (EAS) AF: 0.178 AC: 923 AN: 5172

South Asian (SAS) AF: 0.187 AC: 904 AN: 4828

European-Finnish (FIN) AF: 0.173 AC: 1839 AN: 10600

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8797 AN: 67976

Other (OTH) AF: 0.173 AC: 365 AN: 2114

Alfa AF: 0.149 Hom.: 3424

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
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs186037; hg19: chr1-22952386;