rs648464

Positions:

• chr13-33093328-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 0.364 in 151,802 control chromosomes in the GnomAD database, including 10,252 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 0.36 (10252 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55258 AN: 151684 Hom.: 10253 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.364 AC: 55258 AN: 151802 Hom.: 10252 Cov.: 31 AF XY: 0.367 AC XY: 27213 AN XY: 74148

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.357

Alfa AF: 0.361 Hom.: 7611

Bravo AF: 0.353

Asia WGS AF: 0.406 AC: 1407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs648464; hg19: chr13-33667465; COSMIC: COSV69346349;