rs4810479

chr20-45916409-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;