chr22-19703979-T-C

Variant names:

• chr22-19703979-T-C
• rs4819833

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 0.699 in 152,164 control chromosomes in the GnomAD database, including 37,800 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 0.70 (37800 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 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: 0.699 AC: 106235 AN: 152046 Hom.: 37748 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.699 AC: 106343 AN: 152164 Hom.: 37800 Cov.: 33 AF XY: 0.691 AC XY: 51413 AN XY: 74378

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.679

Alfa AF: 0.662 Hom.: 44029

Bravo AF: 0.717

Asia WGS AF: 0.639 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4819833; hg19: chr22-19691502;