22-38283775-G-T

Variant names:

• chr22-38283775-G-T
• rs5750576

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 0.489 in 152,028 control chromosomes in the GnomAD database, including 18,440 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 0.49 (18440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.489 AC: 74269 AN: 151910 Hom.: 18412 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.489 AC: 74353 AN: 152028 Hom.: 18440 Cov.: 32 AF XY: 0.489 AC XY: 36332 AN XY: 74326

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.457

Alfa AF: 0.456 Hom.: 17329

Bravo AF: 0.485

Asia WGS AF: 0.552 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5750576; hg19: chr22-38679781;