rs4845783

chr1-152520083-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 0.792 in 152,116 control chromosomes in the GnomAD database, including 48,172 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 0.79 (48172 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.791 AC: 120301 AN: 151998 Hom.: 48109 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.792 AC: 120422 AN: 152116 Hom.: 48172 Cov.: 31 AF XY: 0.794 AC XY: 58996 AN XY: 74342

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.789

Alfa AF: 0.735 Hom.: 40378

Bravo AF: 0.799

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.8
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845783; hg19: chr1-152492559;