19-23286164-A-C

Variant names:

• chr19-23286164-A-C
• rs431270

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 0.458 in 151,864 control chromosomes in the GnomAD database, including 18,088 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 0.46 (18088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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: 0.458 AC: 69441 AN: 151746 Hom.: 18033 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.458 AC: 69556 AN: 151864 Hom.: 18088 Cov.: 32 AF XY: 0.459 AC XY: 34038 AN XY: 74236

African (AFR) AF: 0.672 AC: 27840 AN: 41420

American (AMR) AF: 0.460 AC: 7011 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1265 AN: 3460

East Asian (EAS) AF: 0.843 AC: 4329 AN: 5134

South Asian (SAS) AF: 0.464 AC: 2225 AN: 4798

European-Finnish (FIN) AF: 0.324 AC: 3420 AN: 10560

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22200 AN: 67938

Other (OTH) AF: 0.412 AC: 871 AN: 2112

Alfa AF: 0.378 Hom.: 14928

Bravo AF: 0.477

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.27
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs431270; hg19: chr19-23468966;