22-50538325-T-C

Variant names:

• chr22-50538325-T-C
• rs131788

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;