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. The variant received -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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.868 AC: 36027 AN: 41512

American (AMR) AF: 0.877 AC: 13412 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3152 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4674 AN: 5180

South Asian (SAS) AF: 0.911 AC: 4396 AN: 4826

European-Finnish (FIN) AF: 0.903 AC: 9566 AN: 10594

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58597 AN: 68020

Other (OTH) AF: 0.863 AC: 1820 AN: 2110

Alfa AF: 0.865 Hom.: 197287

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4845552; hg19: chr1-153479998;