chr19-34232827-C-T

Variant names:

• chr19-34232827-C-T
• rs629018

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 0.635 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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

African (AFR) AF: 0.769 AC: 31792 AN: 41344

American (AMR) AF: 0.588 AC: 8953 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2111 AN: 3460

East Asian (EAS) AF: 0.164 AC: 840 AN: 5118

South Asian (SAS) AF: 0.445 AC: 2132 AN: 4790

European-Finnish (FIN) AF: 0.543 AC: 5703 AN: 10500

Middle Eastern (MID) AF: 0.648 AC: 188 AN: 290

European-Non Finnish (NFE) AF: 0.625 AC: 42473 AN: 67906

Other (OTH) AF: 0.639 AC: 1339 AN: 2094

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs629018; hg19: chr19-34723732;