chr19-22890403-G-A

Position:

• chr19-22890403-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 0.106 in 150,492 control chromosomes in the GnomAD database, including 949 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 0.11 (949 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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 (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.106 AC: 15899 AN: 150386 Hom.: 945 Cov.: 31

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.106 AC: 15916 AN: 150492 Hom.: 949 Cov.: 31 AF XY: 0.106 AC XY: 7813 AN XY: 73436

Gnomad4 AFR AF: 0.0587

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0902

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.118

Alfa AF: 0.123 Hom.: 1632

Bravo AF: 0.101

Asia WGS AF: 0.129 AC: 446 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8111895; hg19: chr19-23073205;