rs4920520

Positions:

• chr1-18603348-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 0.466 in 151,840 control chromosomes in the GnomAD database, including 16,852 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 0.47 (16852 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.466 AC: 70677 AN: 151720 Hom.: 16825 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.466 AC: 70756 AN: 151840 Hom.: 16852 Cov.: 31 AF XY: 0.465 AC XY: 34530 AN XY: 74182

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.464

Alfa AF: 0.470 Hom.: 24389

Bravo AF: 0.453

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4920520; hg19: chr1-18929842;