rs281439

Variant names:

• chr19-10289434-G-C
• rs281439

Your query was ambiguous. Multiple possible variants found:

• chr19-10289434-G-C
• chr19-10289434-G-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 0.723 in 151,946 control chromosomes in the GnomAD database, including 40,203 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 0.72 (40203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 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: 0.723 AC: 109798 AN: 151830 Hom.: 40186 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.723 AC: 109861 AN: 151946 Hom.: 40203 Cov.: 32 AF XY: 0.723 AC XY: 53690 AN XY: 74268

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.758

Alfa AF: 0.659 Hom.: 1917

Bravo AF: 0.718

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	7.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281439; hg19: chr19-10400110; COSMIC: COSV53424150;