chr19-29595100-C-A

Position:

• chr19-29595100-C-A

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 0.428 in 152,032 control chromosomes in the GnomAD database, including 14,149 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 0.43 (14149 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65016 AN: 151912 Hom.: 14140 Cov.: 33

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.428 AC: 65060 AN: 152032 Hom.: 14149 Cov.: 33 AF XY: 0.430 AC XY: 31935 AN XY: 74324

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.462

Alfa AF: 0.420 Hom.: 8467

Bravo AF: 0.437

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10414410; hg19: chr19-30086007;