rs551719

Variant names:

• chr13-72327391-T-C
• rs551719

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.909 AC: 37785 AN: 41552

American (AMR) AF: 0.878 AC: 13434 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3470

East Asian (EAS) AF: 0.975 AC: 5052 AN: 5184

South Asian (SAS) AF: 0.945 AC: 4561 AN: 4824

European-Finnish (FIN) AF: 0.864 AC: 9166 AN: 10610

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55681 AN: 68000

Other (OTH) AF: 0.851 AC: 1798 AN: 2114

Alfa AF: 0.828 Hom.: 85376

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs551719; hg19: chr13-72901529;