rs4819520

Variant names:

• chr22-19751499-G-T
• rs4819520

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 0.184 in 152,144 control chromosomes in the GnomAD database, including 3,097 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 0.18 (3097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 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: 0.184 AC: 28042 AN: 152026 Hom.: 3087 Cov.: 32

Gnomad AFR AF: 0.0813

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.184 AC: 28067 AN: 152144 Hom.: 3097 Cov.: 32 AF XY: 0.186 AC XY: 13824 AN XY: 74360

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0865

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.191

Alfa AF: 0.215 Hom.: 2961

Bravo AF: 0.178

Asia WGS AF: 0.229 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4819520; hg19: chr22-19739022; COSMIC: COSV53456035;