22-32173637-T-C

Variant names:

• chr22-32173637-T-C
• rs5994481

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 0.548 in 151,708 control chromosomes in the GnomAD database, including 25,141 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 0.55 (25141 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82990 AN: 151590 Hom.: 25080 Cov.: 30

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.548 AC: 83114 AN: 151708 Hom.: 25141 Cov.: 30 AF XY: 0.546 AC XY: 40489 AN XY: 74118

African (AFR) AF: 0.827 AC: 34224 AN: 41398

American (AMR) AF: 0.411 AC: 6266 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3466

East Asian (EAS) AF: 0.346 AC: 1771 AN: 5114

South Asian (SAS) AF: 0.582 AC: 2774 AN: 4770

European-Finnish (FIN) AF: 0.485 AC: 5109 AN: 10528

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 29984 AN: 67862

Other (OTH) AF: 0.486 AC: 1024 AN: 2106

Alfa AF: 0.508 Hom.: 3596

Bravo AF: 0.547

Asia WGS AF: 0.525 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.22
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5994481; hg19: chr22-32569624;