22-16952320-T-G

Variant names:

• chr22-16952320-T-G
• rs4819923

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 0.393 in 152,044 control chromosomes in the GnomAD database, including 11,863 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 0.39 (11863 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 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: 0.394 AC: 59805 AN: 151926 Hom.: 11862 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.393 AC: 59824 AN: 152044 Hom.: 11863 Cov.: 33 AF XY: 0.393 AC XY: 29191 AN XY: 74306

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.400

Alfa AF: 0.408 Hom.: 6826

Bravo AF: 0.393

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4819923; hg19: chr22-17433210;