22-50671564-T-C

Position:

• chr22-50671564-T-C

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 0.502 in 151,890 control chromosomes in the GnomAD database, including 20,284 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 0.50 (20284 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -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 = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76254 AN: 151772 Hom.: 20282 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.502 AC: 76279 AN: 151890 Hom.: 20284 Cov.: 31 AF XY: 0.492 AC XY: 36511 AN XY: 74236

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.0858

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.514

Alfa AF: 0.491 Hom.: 3728

Bravo AF: 0.502

Asia WGS AF: 0.258 AC: 900 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	0.27
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9628185; hg19: chr22-51109992;