22-32173637-T-C

Variant names:

• chr22-32173637-T-C
• rs5994481

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 0.548 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.547 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

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.486

Alfa AF: 0.498 Hom.: 3329

Bravo AF: 0.547

Asia WGS AF: 0.525 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5994481; hg19: chr22-32569624;