chr19-34232827-C-T

Variant names:

• chr19-34232827-C-T
• rs629018

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 0.635 in 151,640 control chromosomes in the GnomAD database, including 31,686 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 0.63 (31686 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96120 AN: 151522 Hom.: 31638 Cov.: 28

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.635 AC: 96227 AN: 151640 Hom.: 31686 Cov.: 28 AF XY: 0.624 AC XY: 46220 AN XY: 74082

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.639

Alfa AF: 0.632 Hom.: 6579

Bravo AF: 0.642

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs629018; hg19: chr19-34723732;