22-38284355-T-C

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 0.83 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

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 = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.809

Alfa AF: 0.797 Hom.: 73231

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135737; hg19: chr22-38680361;