chr19-22560056-G-A

Position:

• chr19-22560056-G-A

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 0.172 in 151,976 control chromosomes in the GnomAD database, including 6,192 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 0.17 (6192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26133 AN: 151858 Hom.: 6167 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.172 AC: 26210 AN: 151976 Hom.: 6192 Cov.: 32 AF XY: 0.169 AC XY: 12540 AN XY: 74302

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.0934

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0879

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0387 Hom.: 1379

Bravo AF: 0.193

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.071
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9305000; hg19: chr19-22742858;