22-38283775-G-T

Variant names:

• chr22-38283775-G-T
• rs5750576

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.525 AC: 21749 AN: 41452

American (AMR) AF: 0.445 AC: 6794 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1384 AN: 3464

East Asian (EAS) AF: 0.683 AC: 3528 AN: 5162

South Asian (SAS) AF: 0.389 AC: 1873 AN: 4818

European-Finnish (FIN) AF: 0.543 AC: 5750 AN: 10580

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31849 AN: 67964

Other (OTH) AF: 0.457 AC: 968 AN: 2116

Alfa AF: 0.460 Hom.: 25606

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs5750576; hg19: chr22-38679781;