19-35289948-A-G

Position:

• chr19-35289948-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 0.382 in 151,912 control chromosomes in the GnomAD database, including 11,165 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 0.38 (11165 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 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: 0.382 AC: 57980 AN: 151794 Hom.: 11168 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.382 AC: 58009 AN: 151912 Hom.: 11165 Cov.: 31 AF XY: 0.381 AC XY: 28304 AN XY: 74232

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.410

Alfa AF: 0.376 Hom.: 14516

Bravo AF: 0.380

Asia WGS AF: 0.378 AC: 1314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.58
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10402233; hg19: chr19-35780851;