chr19-33831232-A-G

Variant names:

• chr19-33831232-A-G
• rs11084753

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 0.644 in 151,984 control chromosomes in the GnomAD database, including 31,790 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 0.64 (31790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.644 AC: 97790 AN: 151866 Hom.: 31778 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.644 AC: 97847 AN: 151984 Hom.: 31790 Cov.: 32 AF XY: 0.641 AC XY: 47632 AN XY: 74284

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.624

Alfa AF: 0.662 Hom.: 41613

Bravo AF: 0.643

Asia WGS AF: 0.482 AC: 1680 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	0.063
DANN	Benign	0.075

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11084753; hg19: chr19-34322137;