rs1873288

chr13-85306989-G-Achr13-85306989-G-Cchr13-85306989-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 0.784 in 151,932 control chromosomes in the GnomAD database, including 47,117 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 0.78 (47117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 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: 0.784 AC: 118992 AN: 151814 Hom.: 47078 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.784 AC: 119073 AN: 151932 Hom.: 47117 Cov.: 32 AF XY: 0.777 AC XY: 57694 AN XY: 74242

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.786

Alfa AF: 0.808 Hom.: 64714

Bravo AF: 0.782

Asia WGS AF: 0.732 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.097
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1873288; hg19: chr13-85881124;