rs629359

Variant names:

• chr19-23439705-G-A
• rs629359

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 0.338 in 151,918 control chromosomes in the GnomAD database, including 9,904 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 0.34 (9904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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: 0.338 AC: 51262 AN: 151800 Hom.: 9869 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.338 AC: 51342 AN: 151918 Hom.: 9904 Cov.: 32 AF XY: 0.334 AC XY: 24764 AN XY: 74236

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.306

Alfa AF: 0.303 Hom.: 978

Bravo AF: 0.345

Asia WGS AF: 0.345 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs629359; hg19: chr19-23622507;