19-35347840-A-G

Position:

• chr19-35347840-A-G

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 0.107 in 152,260 control chromosomes in the GnomAD database, including 1,183 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 0.11 (1183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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: 0.107 AC: 16237 AN: 152142 Hom.: 1170 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.107 AC: 16290 AN: 152260 Hom.: 1183 Cov.: 32 AF XY: 0.108 AC XY: 8072 AN XY: 74464

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0795 Hom.: 334

Bravo AF: 0.108

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10423648; hg19: chr19-35838743;