22-38284355-T-C

Variant names:

• chr22-38284355-T-C
• rs135737

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 0.83 in 152,008 control chromosomes in the GnomAD database, including 52,514 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 0.83 (52514 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.884 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: 0.830 AC: 126035 AN: 151890 Hom.: 52459 Cov.: 30

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.830 AC: 126152 AN: 152008 Hom.: 52514 Cov.: 30 AF XY: 0.830 AC XY: 61680 AN XY: 74288

African (AFR) AF: 0.891 AC: 36944 AN: 41444

American (AMR) AF: 0.852 AC: 12994 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3472

East Asian (EAS) AF: 0.894 AC: 4624 AN: 5174

South Asian (SAS) AF: 0.734 AC: 3540 AN: 4820

European-Finnish (FIN) AF: 0.831 AC: 8783 AN: 10568

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 54003 AN: 67966

Other (OTH) AF: 0.809 AC: 1702 AN: 2104

Alfa AF: 0.806 Hom.: 175930

Bravo AF: 0.840

Asia WGS AF: 0.828 AC: 2880 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	4.7
DANN	Benign	0.81
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs135737; hg19: chr22-38680361;