rs551719

chr13-72327391-T-C

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 0.861 in 152,260 control chromosomes in the GnomAD database, including 56,602 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 0.86 (56602 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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: 0.860 AC: 130896 AN: 152142 Hom.: 56538 Cov.: 34

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.861 AC: 131020 AN: 152260 Hom.: 56602 Cov.: 34 AF XY: 0.866 AC XY: 64466 AN XY: 74464

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.851

Alfa AF: 0.824 Hom.: 66495

Bravo AF: 0.862

Asia WGS AF: 0.956 AC: 3324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.3
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs551719; hg19: chr13-72901529;