rs513464

Variant names:

• chr1-47515324-A-G
• rs513464

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.902 in 152,194 control chromosomes in the GnomAD database, including 62,297 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 0.90 (62297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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: 0.902 AC: 137126 AN: 152076 Hom.: 62249 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.902 AC: 137229 AN: 152194 Hom.: 62297 Cov.: 31 AF XY: 0.901 AC XY: 67075 AN XY: 74408

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.906

Alfa AF: 0.904 Hom.: 12628

Bravo AF: 0.890

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	19
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs513464; hg19: chr1-47980996;