19-23896759-A-G

Variant names:

• chr19-23896759-A-G
• rs723352

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.299 AC: 12402 AN: 41448

American (AMR) AF: 0.134 AC: 2056 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.0753 AC: 390 AN: 5176

South Asian (SAS) AF: 0.0609 AC: 294 AN: 4828

European-Finnish (FIN) AF: 0.0507 AC: 538 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0356 AC: 2421 AN: 68002

Other (OTH) AF: 0.117 AC: 247 AN: 2116

Alfa AF: 0.0573 Hom.: 842

Bravo AF: 0.137

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs723352; hg19: chr19-24079561;