rs1547721

Positions:

• chr13-20293921-G-A

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 0.326 in 151,900 control chromosomes in the GnomAD database, including 9,067 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 0.33 (9067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 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: 0.326 AC: 49510 AN: 151782 Hom.: 9056 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.326 AC: 49564 AN: 151900 Hom.: 9067 Cov.: 31 AF XY: 0.328 AC XY: 24317 AN XY: 74228

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.332

Alfa AF: 0.379 Hom.: 5740

Bravo AF: 0.306

Asia WGS AF: 0.457 AC: 1587 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	0.12
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547721; hg19: chr13-20868060;