rs4845552

Variant names:

• chr1-153507522-G-A
• rs4845552

Your query was ambiguous. Multiple possible variants found:

• chr1-153507522-G-A
• chr1-153507522-G-C

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 0.872 in 152,214 control chromosomes in the GnomAD database, including 57,969 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 0.87 (57969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.888 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: 0.872 AC: 132661 AN: 152096 Hom.: 57921 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.872 AC: 132765 AN: 152214 Hom.: 57969 Cov.: 32 AF XY: 0.875 AC XY: 65089 AN XY: 74426

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.863

Alfa AF: 0.864 Hom.: 85514

Bravo AF: 0.867

Asia WGS AF: 0.913 AC: 3174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845552; hg19: chr1-153479998;