19-22873544-T-G

Position:

• chr19-22873544-T-G

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 0.205 in 152,180 control chromosomes in the GnomAD database, including 3,756 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 0.20 (3756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.205 AC: 31148 AN: 152062 Hom.: 3748 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.205 AC: 31196 AN: 152180 Hom.: 3756 Cov.: 32 AF XY: 0.202 AC XY: 15010 AN XY: 74402

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.219

Alfa AF: 0.121 Hom.: 271

Bravo AF: 0.213

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7246967; hg19: chr19-23056346;