chr22-50538325-T-C

Position:

• chr22-50538325-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 0.775 in 152,056 control chromosomes in the GnomAD database, including 46,072 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 0.78 (46072 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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: 0.775 AC: 117767 AN: 151938 Hom.: 46036 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.775 AC: 117861 AN: 152056 Hom.: 46072 Cov.: 31 AF XY: 0.782 AC XY: 58101 AN XY: 74330

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.746

Alfa AF: 0.727 Hom.: 6359

Bravo AF: 0.775

Asia WGS AF: 0.918 AC: 3193 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	0.83
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs131788; hg19: chr22-50976754;