19-35231835-C-T

Position:

• chr19-35231835-C-T

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 0.824 in 150,122 control chromosomes in the GnomAD database, including 51,460 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 0.82 (51460 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.824 AC: 123678 AN: 150020 Hom.: 51429 Cov.: 26

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.824 AC: 123755 AN: 150122 Hom.: 51460 Cov.: 26 AF XY: 0.827 AC XY: 60636 AN XY: 73350

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.860

Alfa AF: 0.809 Hom.: 2421

Bravo AF: 0.819

Asia WGS AF: 0.778 AC: 2705 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.093
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs554313; hg19: chr19-35722738;