chr22-37586005-A-C

Variant names:

• chr22-37586005-A-C
• rs12157904

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 0.107 in 152,176 control chromosomes in the GnomAD database, including 2,040 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 0.11 (2040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.107 AC: 16216 AN: 152058 Hom.: 2031 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0741

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

GnomAD4 genome AF: 0.107 AC: 16257 AN: 152176 Hom.: 2040 Cov.: 32 AF XY: 0.107 AC XY: 7952 AN XY: 74394

African (AFR) AF: 0.293 AC: 12151 AN: 41442

American (AMR) AF: 0.0861 AC: 1316 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5182

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4824

European-Finnish (FIN) AF: 0.0137 AC: 146 AN: 10628

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0160 AC: 1088 AN: 68034

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0490 Hom.: 2179

Bravo AF: 0.122

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12157904; hg19: chr22-37982012;