22-38283775-G-T

Position:

• chr22-38283775-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;