4-4870520-A-G

Variant names:

• chr4-4870520-A-G
• rs4473606

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 0.645 in 152,132 control chromosomes in the GnomAD database, including 32,093 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 0.65 (32093 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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: 0.645 AC: 98049 AN: 152014 Hom.: 32040 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.645 AC: 98156 AN: 152132 Hom.: 32093 Cov.: 33 AF XY: 0.649 AC XY: 48260 AN XY: 74384

African (AFR) AF: 0.738 AC: 30645 AN: 41512

American (AMR) AF: 0.647 AC: 9896 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2354 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3728 AN: 5168

South Asian (SAS) AF: 0.562 AC: 2708 AN: 4818

European-Finnish (FIN) AF: 0.676 AC: 7157 AN: 10590

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39758 AN: 67976

Other (OTH) AF: 0.621 AC: 1311 AN: 2110

Alfa AF: 0.609 Hom.: 72957

Bravo AF: 0.646

Asia WGS AF: 0.615 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.46
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4473606; hg19: chr4-4872247;