rs4810479

Variant names:

• chr20-45916409-C-T
• rs4810479

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 0.671 in 152,116 control chromosomes in the GnomAD database, including 35,050 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 0.67 (35050 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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: 0.672 AC: 102080 AN: 151998 Hom.: 35044 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.671 AC: 102103 AN: 152116 Hom.: 35050 Cov.: 33 AF XY: 0.664 AC XY: 49393 AN XY: 74344

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.674

Alfa AF: 0.727 Hom.: 81239

Bravo AF: 0.655

Asia WGS AF: 0.408 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810479; hg19: chr20-44545048;