rs648464

Variant names:

• chr13-33093328-G-A
• rs648464

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;