19-23896759-A-G

Position:

• chr19-23896759-A-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 0.122 in 152,160 control chromosomes in the GnomAD database, including 2,111 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 0.12 (2111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.122 AC: 18577 AN: 152042 Hom.: 2107 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0356

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.122 AC: 18616 AN: 152160 Hom.: 2111 Cov.: 32 AF XY: 0.122 AC XY: 9062 AN XY: 74394

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.0753

Gnomad4 SAS AF: 0.0609

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.0356

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0715 Hom.: 189

Bravo AF: 0.137

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723352; hg19: chr19-24079561;